oh man sonic the timeline
Before I write anything about the storyline of the Sonic the Hedgehog series, I always feel I must point out that, when it comes to all of its many elements, the storyline ranks below pretty much everything else. Gameplay, level design, visual style...if none of that works, it doesn't matter if the game reveals all the secrets of SONIC'S SECRET PAST!!1! if it's a bad game. However, I'm pretty sure anyone who comes to Retro already knows this, so it doesn't hurt to occasionally nerd out about the timeline and nuances of Sonic canon. Lord knows I've done it on more than one occasion. That disclaimer is more for people who only care about mapping out Shadow's convoluted history.
What's also important to point out is the fluidity that Sonic Team has for the timeline, which has also been mentioned prior in this thread. There's a reason that, way back when AAUK was working at Sega, he told everyone that Sonic and the Secret Rings wasn't canon, then was immediately contradicted when it was referenced in Sonic Generations. Really, it's just like how a comic book should be - you have over 75 years of history for Superman, go ahead and reference what you want, but don't feel like you must be a slave to the smallest details. Maintain the history, don't fret about the continuity. Weird to think about? Yes, but it's the only way for a franchise that has been around for decades and had multiple people involved to stay consistent.
With all that said, let's jump into the classic timeline. Really, my opinions don't differ all that far from what other people have said.
Sonic the Hedgehog --> Sonic CD --> Sonic 2 --> Sonic 3 & Knuckles
oh man controversial statement. Sonic CD seems to be the one that's moved around the most, but one must remember that the team behind CD were developing a sequel to Sonic 1, just like the team to Sonic 2 were. The fact that Amy is at Little Planet but not in Sonic 2 or 3 is not really all that odd. She didn't follow Sonic to Never Lake, the tarot cards told her that she would have a "destined encounter" with him there. Which is what happened - she traveled to the Little Planet on her own, found Sonic, got kidnapped, and was a goal that Sonic needed to strive after to restore balance to the locale. Would Sonic have saved the Good Future if she wasn't there? Sure. Would he have fought Metal Sonic if she wasn't kidnapped? Probably. But the tarot cards did not lead her to Westside or Angel Island, and they certainly didn't lead her to seeing Sonic in Adventure. She was already living in Station Square when he came to vacation there.
But what about Metal Sonic? Well, yes, the robotic Sonic that features in CD looks far more advanced than the ones featured in Sonic 2 and Sonic 3. But, consider this. While Metal does have certain attacks he can use, the time Sonic and his metallic doppelganger face together is primarily a race. They never go head to head in a physical bout. Sonic doesn't try to jump on his head, instead he wants to prove to Eggman that no mechanical creation can best his natural speed. Sonic CD, more than any other classic game, focuses on the natural/industrial themes that are merely window dressing in the other titles. Metal's attacks are more to slow the real Sonic down, not to outright kill him (though that can happen if you're not careful). And what happens when Sonic wins? Metal self destructs by running into a wall. Which, well, shows he really isn't all that strong of a foe. Eggman sacrificed durability for speed, because the end game was for Eggman to kill Sonic himself with his death ray coming out of the bottom of his Eggmobile in Stardust Speedway. Eggman was hoping Sonic would be bested by his own creation, that the wall would fall (which Sonic wasn't expecting) and in the confusion not be able to avoid Eggman's direct attack.
So why does Mecha Sonic look so much clunkier, so less advanced? He definitely has the feel of a prototype in Sonic 2, and had significant upgrades in Sonic 3 & Knuckles. I used to think "oh, Eggman must have just pulled out a prototype that he made before creating Metal Sonic and used that as a stopgap measure before confronting him in his mech," but now I think it could really be a prototype he created after Metal. Instead of focusing on a speed-based creation which failed spectacularly, he was experimenting with replicating another aspect of Sonic - his durability, his strength. After all, Sonic can best nearly all of Eggman's creations with a well-placed hit, and Mecha Sonic? Takes eight. Mecha isn't trying to run against Sonic, he is more concerned with combat. He looks so basic in Sonic 2 probably because Eggman was more concerned with building the Death Egg and collecting the Chaos Emeralds than he was with building another robot Sonic. Come time for Sonic 3, the Death Egg is already built, and Knuckles is there helping out with his schemes. He has more time to refine the design he was toying with in Sonic 2.
If we take into account Sonic 4, then it's really a case of the strength-based robot Sonic failing twice, so Eggman goes back to his original design and decides to "upgrade" him to be more than just a robot that runs fast. The scene in Sonic 4 is already contradictory in the sense that Metal Sonic is in one piece while he was in many pieces at the end of Stardust Speedway, so really the scene is an afterthought using previously-available resources instead of being slavish to the plot of Sonic CD. Which can also apply to the Little Planet's use in Sonic 4 Episode II as a whole.
So taking all of that into account, it makes far more sense for Sonic CD to be the second part of the classic games. Now, when it comes to the Game Gear games...well, the problem there is that most of them just don't fit into the overall narrative. They were created by a separate team, with separate goals, and didn't really pay that much attention to what Sonic Team was doing. When Aspect took over the portable franchise, they really didn't spend much time trying to emulate what the other games were doing. Yes, we had nods to Sonic CD with the peel-out, we had Knuckles show up in Sonic & Tails 2, but none of it really gels with the main games, at least storyline wise. Visually, yes, it all looks like something from the world of Sonic. If there was a bit more communication, then the games could have had stories that didn't blatantly contradict what was happening elsewhere.
The biggest source of contention? The Chaos Emeralds. In the original Sonic, as well as the 8-bit version, there were only six. With the 16-bit Sonic 2, it's revealed there are seven, a number that remains consistent through the rest of the main series, even to this day. In every Game Gear game, both the pro and antagonists are still concerned with collecting only six. The storyline to the 8-bit Sonic 2, if we wanted a single canon, can not happen before the 16-bit Sonic 2. The Japanese manual explains how Sonic & Tails met, which was on West Side Island, and was only a couple of days before Eggman began his siege there. There's no room for Sonic & Tails to become friends and go back to South Island (Tails only discovers the Tornado exists minutes before Eggman shows up and talks about how he knew following Sonic around would lead him to the Chaos Emeralds, even though Sonic didn't even know the Emeralds were now on the island, the story really pushing the fact that coincidence is the order of the day), which means there's no time for Eggman to kidnap Tails, or even know he exists before the game happens.
There is also no room for anything to happen between Sonic 2 and 3, the Japanese story stating that a few days pass between Tails seeing a "huge wave" in the ocean (Angel Island crashing) and picking up a strange reading on his newest invention, the Jewel Radar. Remember, at that point, Sonic has all seven Chaos Emeralds, so reading anything on his radar would send up red flags, and Eggman probably hasn't had time to leave Angel Island just to antagonize Sonic. He may be a childish evil genius, but if his grand plan was just thwarted, even he would spend a few days to regroup, especially if he's on an island of legend, needs to trick its guardian into thinking he's a good guy, begin repairs on the Death Egg, build up a new badnik army, and work on the Mecha Sonic project again. There's no time to go back to South Island and kidnap Tails. There's no point! Better for Sonic & Tails to think Eggman is out of commission while he works on his next grand scheme.
That means the 8-bit version of Sonic 2 could happen no earlier than after Sonic 3 & Knuckles, which means that Sonic (a traveler by nature) just lives on South Island, Tails now lives there too, and Eggman only cares about six emeralds instead of seven. Come time for Sonic Chaos, it's still six, and they are somehow linked to South Island, the manual stating it's the resting place of the Emeralds (even though they've now been on three islands), and hinting that because Eggman gained one, it's somehow thrown everything out of balance and causing South Island to sink into the sea. Triple Trouble, you have Knuckles show up again and has the same antagonistic relationship with Sonic, even though he should know Eggman is bad and Sonic is good. When Eggman tricks Knuckles in Sonic Adventure, he's trying to make Knuckles think that Sonic is collecting the shards of the Master Emerald, something Knuckles has a hard time swallowing until the sees Sonic with the green Chaos Emerald and jumps to conclusions, which after a brief fight and conversation is sorted out. What would Knuckles be trying to do in Triple Trouble? Why would he be on South Island and not Angel Island, caring about the Chaos Emeralds which weren't really a concern for him anymore?
You could try and say "oh, well obviously Knuckles went back to get the Chaos Emeralds because he thought he should guard them with the Master Emerald," which he kinda does in Sonic Adventure. But Sonic doesn't really care if he is guarding them or not. The only reason people want Triple Trouble to be canon is because of Fang the Sniper, since otherwise he isn't part of the story. Unless you want to consider Sonic the Fighters to be part of canon, even though it has eight emeralds in that game, unless the eighth emerald is the Master Emerald, which means it's the most impractical space ship ever built. Oh, side note: the Japanese manual to Triple Trouble points out Fang and Eggman aren't working together. So there's that.
It requires way too much fiddling for the Game Gear games to work with the 16-bit titles, which means it's way easier for them to be their own separate thing. The only one that could work is Tails Adventures, and that's only because it's a Tails solo game that is stated to happen before he meets Sonic. And maybe the Drift games, which would let you have Fang in the main canon.
SegaSonic the Hedgehog, that could take place before or after the first Sonic game. For the person who said it must be before because Sonic is running away, that doesn't work all that well. Sonic takes on Eggman head on, sure, but if some huge robotic creation is there trying to swallow him whole, he's not going to run inside head first, especially if he's with two friends who aren't all that well versed in combat. Or Sonic would try to run around and attack it from another angle, or some such thing. Chaotix? Takes place a couple months after Sonic & Knuckles. Everything involving the Master Emerald and the Chaos Emeralds (which is another post entirely, and one I'm sure I've talked about before on here many years ago) causes part of the Echidna homeland to rise from the depths of the oceans, still having its own secrets. Eggman lands there before Knuckles can explore it, and the other members of the Chaotix arrive for their own personal reasons. They are never an official team, and only decide to sometime between the 32X game and Heroes. And you can ignore Charmy, because there's no way the average person doesn't know who Dr. Eggman is in Heroes after he BLEW UP HALF THE MOON in the previous game.
So including my personal preference of not wanting a Sonic game to take place before the original...
Tails Adventures --> Sonic the Hedgehog --> SegaSonic the Hedgehog --> Sonic CD --> Sonic 2 --> Sonic 3 & Knuckles --> Knuckles' Story --> Sonic 4 Ep. 1 & 2 --> Chaotix --> Flickies' Island --> Sonic the Fighters --> Sonic R --> Sonic Pocket Adventure --> Sonic Adventure
I could go on past Adventure, but this post is already long enough without trying to dissect Shadow's backstory or figuring out where the Advance games slip in to the main titles or understand the madness of Eggman Nega. So yeah, there you go. Oh, and Spinball can't work. It's tied too deeply into the western cartoons to really work as part of the games canon.