I would've much preferred if they'd not just said "one level per game" and threw out all but one level in all the games, even the ones with multiple great and memorable levels. But playing by that rule and using all my skill in general super-dickery and finding a way around rules....
First, 16-bits, retcons in the same era, etc.:
1: Scrap Brain
2: Hidden Palace, re-interpreted into being much more like 3's version in later areas.
3: Launch Base
&K: Sandopolis
Knux in 2: Chemical Plant
4: Lost Labyrinth, re-interpreted to more or less be Labyrinth Zone, which it was supposed to be anyway.
CD: Stardust Speedway
Spinball: Toxic Caves, except like an ordinary Sonic game, with pinball stuff being demoted to an occasional gimmick here and there.
Crackers/Chaotix: Crackers has two levels, both tiny, glitchy, and all around poorly done. But from Chaotix, Techno Tower.
8-bits:
1: Sky Base
2: Scrambled Egg
Triple Trouble: Atomic Destroyer
Chaos: Electric Egg
Can't easily find the other 8-bit level lists or even reference to the games themselves, but I think there are more.
Misc. 2D/2Dish:
Rivals: Meteor Base
Rivals 2: Blue Coast
Can't find the misc. 2D/2Dish ones easily, either.
Early 3D ones:
Fighters: Death Egg's Eye, re-interpreted to more or less be Death Egg from 3&K.
3D Blast: Panic Puppet
Shuffle: Emerald Coast, re-interpreted as more like the actual level from Adventure rather than a sort of virtual game board.
Pretty sure there are quite a few more here, too, but can't find them.
Adventures & similar:
Adventure: Ice Cap, re-interpreted to be basically good ol' 3's Ice Cap.
Adventure 2: Final Chase
Shadow: Central City
Heroes: Egg Fleet
'06:
Advance series:
Advance: Egg Utopia
Advance 2: Hot Canyon
Advance 3: Chaos Angel
Collector packs just for the sake of more levels:
Jam: Sky Sanctuary
Mega Collection: The Machine, with pinball stuff demoted to an occasional gimmick like in Toxic Caves.
Gems Collection: Gene Gadget
Riders:
Can't find Free Riders or the original, but...
Riders ZG: 90's Boulevard
Recent ones:
Unleashed: Empire City
Colors: Starlight Carnival
Aaand....
Generations: Not self-referential per se, no. Just a final level never done before. If Sonic Team had any idea that Sega was about to implode and Sonic was about to change forever and so on, rather than the plot being about something monstrous gobbling up all that's happened in the past purely coincidentally, they should've made Generations a definite and clear end to the old way of things. A black void, with occasional white lines and glowing multi-colored lights to follow, very little music and what is there consisting mostly of sudden, rather startling sounds conflicting with low, smooth, but still simply unnerving rumbles and hums. Interface and control screws of some sort. The occasional flash across the screen of Sonic's memories, that may very well no longer be when it's all said and done with. Something that really gives the impression the time eater has genuinely gobbled up all of Sonic's personal timeline, and perhaps even much more. Something very frightening. Both Eggmans floating high overhead, too high to reach, relentlessly taunting the Sonic mismatched to them with their sarcastic and monstrous quips as the level drags on: old Eggman to new Sonic and new Eggman to old Sonic. And everything screaming, though obviously not outright saying due to it technically being a children's game, one simple fact: "Your world is dead. All that you knew is gone, Sonic."
And, to top it all off? You'll notice Green Hill didn't appear on the list I thought up, above. There's a reason why I thought it up like that: Save the best for last. This is Green Hill. Or what's left of it. Amid the already terrifying void, small, distorted bits of the theme can occasionally be heard, and little bits of its lovely green grass and curves and rock and bridges and so on can be seen laying about in the horribly ruined Green Hill Zone. A few of the classical-looking palm trees spring out of seemingly insane places and twist and contort and sway and throb in completely unnatural and wrong ways. On top of both Eggmans insulting both Sonics, it seems like the Time Eater itself is. And at the end, a small puddle of water, followed by some sand down the path, and a small bit of seemingly unruined forest that looks different from the bits hanging around elsewhere in the void. Floating a bit off the bottom of the sickening, offensive void. All that's left of the floating island, which was once nearby in the Ocean to the island Green Hill sits on. And at its core, over a tiny little pointed rock reminiscent of the mountain, as obliterated bits of slightly stained and heavily overgrown Sky Sanctuary marble float just over Sonic's head, and mechanical shards of the Death Egg float just above that confirming that it was indeed once Angel Island...
The master emerald. And suddenly, it's completely broken to dust. Not shards. Not anything Knuckles could hope to put back together. Dust. And then the time eater decides to blow a foul wind from nowhere and blow the dust away forever, right before Sonic's own eyes.
