(I know that Toei, when they created Dragon Ball GT, haxed Goku to the point of no return, but I still want to explain Goku's power level in GT. If you have any questions, please ask them below.)
So, let's get started.
At the End of Dragon Ball Z, it was implied that Goku was the strongest being in the universe as, apparently, while fighting Uub, he was fighting him evenly. Since Uub is the reincarnation of Kid Buu, we can imagine that EoZ Goku is equal to Kid Buu Saga SSj3 Goku, who was twice as strong as Buu Saga SSj3 Goku. Assuming that Goku transformed into his transformations, this would mean that...
EoZ Base Goku=Buu Saga SSj3 Goku
EoZ SSj Goku>SSj2 Gotenks (Post-RoSaT)
EoZ SSj2 Goku=SSj3 Gotenks (Post-RoSaT)
EoZ SSj3 Goku>=Ultimate Gohan
For another point of reference, during the fight with Buuhan, Vegito was able to rival Buuhan in his base form (This was seen in the filler, but if this appeared in the manga, Vegito's so strong that if he fought Buuhan in his base form, he'd still beat Buuhan). When he transformed into Super Vegito, he started to make Buuhan's attacks look like a joke. The strange thing, though, is that both the anime and the manga imply that Vegito was holding back a lot of power. This can be seen because, in the Daizenshuu, Super Vegito is said to be three times stronger than Buuhan. In the anime, Base Vegito=Buuhan, so Super Vegito>>Buuhan. This is important because I'll be talking about a Full Power Super Vegito, who is many, MANY times stronger than Buuhan.
Let's say that Buuhan is one.
Vegito (holding back): 1
Super Vegito (still holding back): 3
Full Power Vegito: 10
Full Power Super Vegito: 1,000
Now, to Dragon Ball GT...
Black Star Dragonball Saga
At the Beginning of GT, we watched a fight between Goku and a now grown-up Uub. The narrator said that it was, according to the Funimation Dub, 10 years after the EoZ. Now, back in the Cell Games saga, we learned that, thanks to the Hyperbolic Time Chamber, Goku, Gohan, Vegeta, Trunks, and Piccolo all went from people who couldn't even touch Android 17 and Android 18 to guys who could evenly fight Perfect Cell. Now, imagine Goku's strength 20 years after the Kid Buu Saga, which took place around 7 years after the Cell Saga, so around 27 years after the Cell Saga. Even if one used the Japanese Dub, that still means that GT began 15 years after the Kid Buu Saga.
At this point, Goku's strength is almost indescribable. One could say that Goku now exceeds Super Buu, as it's implied that he is stronger than his EoZ SSj3 counterpart.
And that strength only rises when he fights strong opponents, like Ledgic, Cardinal Mutchy Mutchy, and Luud. All three antagonists were stronger than Majin Buu (let's say, around Buutenks level), so Goku was often times pushed to the breaking point. As a result, his body gained massive powerups due to the Zenkais caused from him fighting the antagonists.
His strength increases more when he turns into a Super Saiyan. The first time he ascended into a Super Saiyan in GT, during the fight against Ledgic, his power skyrocketed manyfold. Because Goku had learned to master his Super Saiyan transformation during the Cell Saga, the multiplier had increased to 100-fold, which means that, if Goku went all-out in his SSj form, he would be 100x stronger than Super Buu. Goku, however, held back against Ledgic, although Ledgic still lost. So, I'd say that during the fight with Ledgic, SSj Goku was 25x stronger than Super Buu.
By the end of the Black Star Dragonball Saga, Goku only gets a lot stronger. By the time he arrived on the Planet M2, I say that he's now around Buuhan's level, who is around 10x stronger than Super Buu.
If we saw Goku transform at the beginning of GT, his power level would be like this.
Goku is stronger than Super Buu in his base. When he transforms into a Mastered Super Saiyan, his strength increases 100-fold, so he 100x stronger than Super Buu, and 5x stronger than Buuhan. When he transforms into a Super Saiyan 2, he is 200x times stronger than Super Buu, and would be around a theoretical Full Power Base Vegito. As a SSj3, he is still 25x weaker than Full Power Super Vegito.
However, if he transformed at the end of the saga, he would be even stronger. Goku as a Super Saiyan would be 100x stronger than Buuhan, and only 10x weaker than Super Vegito. As a Super Saiyan 2, he's 200x stronger than Buuhan, with Super Vegito still 5x stronger than Goku. As a Super Saiyan 3, Goku isn't far off from Super Vegito.
In the beginning of the Baby Saga, when Goku and Trunks have been captured by the Sigma Force, Goku's strength is incredible, around Buuhan's level. When he fights the Sigma Force, at first, it looks like he was struggling with the Sigma Force, but he was only holding back his power. In the Funimation Dub, Nezi stated that, when Goku powered up, his power more than tripled.
When fighting General Rilldo, Goku stated that he was "stronger than Majin Buu." It makes logical since for Goku to mean Buuhan, since that was the strongest Buu. Rilldo was fighting on par with Goku, which supports the implication that Rilldo is stronger than Buuhan. Then, Goku transformed into a Super Saiyan, causing his strength to increase 100-fold. This forced Rilldo to transform into Meta-Rilldo, causing his strength to increase as well. Goku was able to hold the new Rilldo off with ease. Then, Rilldo ascended yet again, into Hyper Meta-Rilldo. That's when Goku started to have problems. Goku was able to hold his ground, but eventually, Rilldo's abilities to manipulate the metal on M2 overwhelmed him.
After escaping M2, Goku gained a massive power-up from the Zenkai he received due to fighting General Rilldo and due to fighting the Sigma Force. His power increases beyond Buuhan's level.
Back on Earth, Baby was able to possess Goten. When SSj Baby Goten fought Gohan, Gohan was able to hold him back in his base form. This is because, according to the Dragon Ball GT Perfect Files, GT Base Gohan had not neglected his training, and had been able to find a way to reach SSj and SSj2 and still be able to gain a Mystic power-up, so GT Base Gohan's strength can be compared to Ultimate Gohan. When he fought Vegeta as a Super Saiyan, he matched SSj Vegeta blow for blow. So, we can assume that Vegeta is twice as strong as Ultimate Gohan.
Then, Goku arrives on Earth. His strength is over 1.25x greater than Buuhan, and likely he can manipulate his power level to 25x higher than his base form. As proof, when he fought SSj Baby Gohan (who is 100x stronger than Ultimate Gohan) and SSj Baby Goten (who is around Super Buu's level), Goku was able to knock both his sons back into base, so this proves that Full Power GT Base Goku is stronger than SSj Gohan but weaker than SSj Vegeta. Then, as things couldn't get dark enough, Baby Vegeta came to the battle.
Now, Goku is as strong as Buuhan, so when he transforms into a Super Saiyan, he is 100x stronger than Buuhan. As a Super Saiyan 2, he is only 5x weaker than Super Vegito. But then, when he reaches Super Saiyan 3, he is only three times stronger than Super Saiyan 2. He would be equal to Super Vegito, except that, unfortunately for Goku, his child-sized body can't handle the stress of the transformation. Since Baby Vegeta in his normal form was making SSj3 Goku look like a child, it can be assumed that normal Baby Vegeta is around Super Vegito's level. That strength only increases when Gohan, Goten, Bulla, and Trunks gave him their energy (which led to Baby transforming into Super Baby Vegeta), causing him to become stronger than anyone else in the universe.
After healing from his injuries and gaining a massive Zenkai power-up due to falling into Suguroku Space, he, Suguro and Suguro's son escaped into the Supreme World of the Kais, where Goku had his tail pulled out. Old Kai implied that having his tail pulled out would mean that, not only would his transformations be more stable, but he would gain a massive power increase. From watching the series several times, I guessed that Goku's power level doubled from having his tail pulled out. It wasn't automatic, but when he transformed into a Super Saiyan 3, his "mystic Saiyan powers" were activated, so he was able to fight Baby for a short while. But since he still lost, his SSj3 form must still be weaker than Final Form Baby Vegeta. Combined with the fact that he received a massive Zenkai, and it looks like, when Goku fought Final Form Baby Vegeta, Goku was 2.5 to 3 times stronger than he was before. So he was the equivalent of three Buuhan's in his base form. As a SSj3, he's now stronger than Super Vegito, possibly up to Super Baby Vegeta.
Then, Goku transformed into a Golden Great Ape, which, as some people, say, is the equivalent of a Super Saiyan and an Oozaru combined. In this case, Goku is 1,000x stronger than he was in base. It seemed like an even fight, against Baby, but Baby was faster and smarter than Goku. Then, SSj4, the condensed and concentrated, and therefore stronger, version of the Golden Oozaru transformation, was born. Super Saiyan 4 multiplies Golden Great Ape by 10. This explains why Goku was able to defeat Final Form Baby Vegeta in this form.
When Baby transformed into a Golden Great Ape, his strength increased to the point that not even Goku's newfound transformation was enough. But when Goku's friends gave their Super Saiyan powers to Goku, Goku was able to reach full strength. At full power, SSj4 Goku was stronger than even Full Power Golden Great Ape Baby Vegeta. After absorbing Baby's Revenge Death Ball, he became 5x stronger than Golden Great Ape Baby Vegeta. He then was able to defeat Baby.
By the end of the saga, Goku was 2.5x stronger than Buuhan. As a Super Saiyan, he is now stronger than Meta-Rilldo. A Super Saiyan 2 Goku would be 2x weaker than Super Vegito, and a Super Saiyan 3 Goku would be 2x stronger than Super Vegito. As a Super Saiyan 4... do I even need to explain?!
Here's a power chain to show this:
GT Base Goku>>Buuhan
GT SSj Goku>>Hyper Meta-Rilldo
GT SSj2 Goku<Super Vegito
GT SSj3~Super Baby Vegeta>Super Vegito
SSj4 Goku > Every. Single. Person from DBZ and Dragon Ball GT up until this point.
Super 17 Saga
At the beginning of the saga, we know that Goku is now eight times stronger he was when he fought Baby, due to the fact that he recovered from the fight, and due to the fact that he trained during the year. We also know that the other fighters, including Vegeta and Gohan (we know Gohan got stronger because Super 17 Saga Gohan was able to hold off General Rilldo, whereas in the Baby Saga, he couldn't even fight Goku as a SSj2), would have also gotten stronger.
When Hell Fighter 17 and Android 17 fused, the fusion was similar in style to the Potara Fusion. The resulting fusion created Super Android 17, an android so powerful, that when Majuub attacked him, 17 didn't even notice. And we know that Majuub was able to damage Final Form Baby Vegeta during the Baby Saga, which means that 17 is stronger than Final Form Baby Vegeta, perhaps around Golden Great Ape Baby Vegeta's level.
So, what about Vegeta? During the fight, it seemed that SSj2 Vegeta did a better job than Majuub did. So, why exactly? Most say that Vegeta received a massive Zenkai. That's only part of the reason. Another reason is that Vegeta had been training for the rest of the year, to the point where he reached Buuhan's level. It's also possible that he also kept the power-up that Baby gave him, so SSj2 Vegeta = Normal Form Baby Vegeta. Then, one other reason is that Super 17 was toying with him.
While all of this was happening, Goku was fighting Cell and Frieza, who were most likely stronger than even Rilldo (why else would Toei keep them in Hell?). Goku was discovered to easily make them look like weaklings, in part because of the power-up he received from having his tail pulled out, and in part because of the fact that he trains a lot.
After defeating Cell and Frieza and escaping Hell, Goku started Round 1 as a Super Saiyan. Because he had access to some of his SSj4 powers, and because 17 was toying with him, Goku launched him across the planet, whereas SSj2 Vegeta was barely able to stand up against him. This proves this SSj Goku is around Normal Form Baby Vegeta's level. But Super 17 literally started to throw him around, so Goku was forced to transform into a Super Saiyan 4.
Now, the Super Saiyan 4 Goku in the Super 17 Saga is stronger than the Super Saiyan 4 Goku in the Baby Saga. Why is that? Simple, the Goku in the Super 17 Saga is stronger than the Goku in the Baby Saga, since the Baby Saga Goku didn't have a tail, and didn't have as much training as the Super 17 Saga Goku. In fact, the show implies that SSj Goku (Super 17 Saga)>>Normal Form Baby Vegeta>>SSj3 Goku (Baby Saga), due to the events that happened before.
After 17 absorbed some of Goku's best attacks, including his 10x Kamehameha, 17 was able to beat down Super Saiyan 4 Goku, so Goku had to resort to using the Final Explosion technique. But 17 survived the blast, and was about to blast him with a Shocking Death Ball. 18, however, arrived and stopped that. 17's defeat came when 18 kept firing many Ki blasts, Goku was able to create a Dragon Fist that blasted a hole right through 17's chest, and then he fired a Kamehameha right through his chest, obliterating him.
If we can study Goku's power level, at this point, it would look like this:
Base Goku >>> Buuhan
SSj Goku >> Normal Form Baby Vegeta
SSj2 Goku >> Super Baby Vegeta
SSj3 Goku >> Final Form Baby Vegeta
SSj4 Goku >> Golden Great Ape Baby Vegeta
Shadow Dragon Saga
Beginning of Saga
At the beginning of the saga, we can say that this saga begins two days after the Super 17 saga, which is an ample amount of time for Goku and his friends to heal. Goku, at this point, is now stronger than he was before, probably equal to the SSj Goku who fought Ledgic.
Goku, if he transformed, would have this chart.
Base Goku~SSj Goku (Imegga)
SSj Goku>Super Baby Vegeta
SSj2 Goku>>Super Baby Vegeta
SSj3 Goku>>Final Form Baby Vegeta
SSj4 Goku~Super 17 (Post-10x Kamehameha absorption.)
Fight against Haze Shenron
Goku would still have the same power level as before, as he basically didn't fight anyone before this Dragon. But since his body suffered damage from the pollution and from the Dragon's attacks, he gains a Zenkai.
Fight against Rage Shenron
During the fight against Rage Shenron, Rage Shenron was implied to be weaker than Goku, as even his most powerful move, the Dragon Thunder Clap, only singed Goku badly. As a Super Saiyan 4, Goku didn't even feel it, so it's possible that Goku didn't even need Super Saiyan 4. Just a normal Super Saiyan could do it. What makes Rage so dangerous, however, is the fact that he can absorb any attack, even a 10x Kamehameha, and "give it back" to an opponent, resulting in some serious damage for the opponent. Goku suffered serious damage during the battle, so he could get a zenkai.
Fight against Oceanus Shenron
Base form Goku, at this point, is now 6x stronger than Buuhan. When he fights Oceanus Shenron, however, not even this would be enough against the six star dragon, since her constant spinning creates a wind-generated shield that prevents anything from damaging here. A Full Force Kamehameha from Goku couldn't do anything.
Fight against Naturon Shenron
During the first fight against Naturon Shenron, Goku and Pan dodged every one of his attacks, and when they land on top of his head, they cause him to blast himself. Naturon escaped the mole body and went inside the Dragon Ball, and so when Pan touched the Dragon Ball, she was absorbed into Naturon.
Naturon was so powerful at this point that Goku was forced to transform into a Super Saiyan 4, which proves that, even though he was weaker than Goku, he still can cause serious damage. Ultimately, Goku had to act like he was defeated to cause Naturon to make a mistake that cost him his life.
Fight against Nova and Eis Shenron
Nova Shenron, when starting the fight, seemed to be halfway as strong as Super Saiyan 4 Goku, since Goku kept getting scared about Nova the whole time. But it was when he reached his true form that Nova finally matched Goku's Super Saiyan 4 form. From watching the fight, it can be said that Goku is also able to match Nova. The only problem is the fact that Nova is faster than Goku.
Eis Shenron isn't as strong as Goku, but it can be said that, if he fought fairly, Eis Shenron would mostly match Goku in strength and speed. But, needless to say, it seems that Eis could only damage Goku when Goku was in a vulnerable spot.
Fight against Syn/Omega Shenron
Syn Shenron, needless to say, is WAY stronger than SSj4 Goku. Goku said that even if he was at full power, he still would lose to Syn, as Syn was able to take a full power 10x Kamehameha to the face and get away unscratched. It was only after his friends helped him surpass his limits that he was able to defeat Syn Shenron.
Then, when Syn Shenron transformed into Omega Shenron, his strength increased 10x, making him 10x stronger than Full Power Super Saiyan 4 Goku. He made SSj4 Goku the first time around look like a joke, and he also made SSj4 Vegeta (who was stronger than a FPSSj4 Goku) look like a joke as well. It took SSj4 Gogeta to break Omega Shenron, and when the fusion failed, it took a Universal Spirit Bomb to finish him off.
End of GT
One hundred years later, Goku is now the strongest being in the universe, as he had fused with the Dragon Balls. His base form now rivals that of Omega Shenron's level at the very least. If he transformed into a Super Saiyan, he would be eight times stronger than SSj4 Gogeta at the Shadow Dragon Saga. He would be wickedly powerful at the end of GT, due to all of his training.