Sonic 1: anything but Marble zone. good grief! But hmm. I guess my only choices are Scrap Brain and Star Light. Scrap Brain it is! (that stage just has more gameplay substance)
Sonic 2: CHEMICAL PLANET *dances*
Sonic 3: Ice Cap is obvious but Carnival Night is also pretty bad (as in good)
Sonic & Knuckles: Lava Reef
Sonic CD: this game has only one stage - Stardust Speedway
Knuckles Chaotix: oh my god, hell yes, Botanic Base
Sonic 3D Blast: I should say Rusty Ruin solely because I used the music for my SonicDIY stage. Plus this stage has neat music even if you play in the Saturn version.
Sonic R: it's all between Radical City and Reactive Factory. I pick Radical City
Sonic Adventure: Here's the thing -- this game doesn't have any great stages. I say Casinopolis because the ducts segment is the only thing that stands out.
Sonic Adventure 2: Pyramid Cave!
Sonic Rush: a sonic game... without any stages. That was a great idea, wasn't it.
Sonic Riders: Ice Factory. one of my favorite aspects is the lane dividers.. IN A FACTORY. But anyway there is a lot to like about this stage, some of the craziest shortcuts, a lot of skill, some wide areas, the cool winding final section, and the giant fan which is sweet, with the awesome super-fast grind rail.
Sonic Heroes: between Hang Castle, Rail Canyon, or Bullet Station.. I say Hang Castle. I have said once before, I'll say it again, the dialogue in-game makes it good. Plus, brilliant music (not to the mention the awesome idea of having the music change) and castles + ghosts = win, no exceptions
Shadow the Hedgehog: Westopolis vs. Lethal Highway. I forgot why I decided it was Westopolis, but it might be because it's more of a true city stage and not a highway. Plus there is so much going on in that stage, it's one of the fastest, and it is the most fun to time attack in the whole game.
Sonic06: See, this game actually has lots of good choices. Anyway, I say Radical Train. Sheer innovation, man.
Sonic Adventure 2: Aquatic Mine
props for picking a Knuckles stage. I like that one, too!
Sonic & Knuckles: Sandopolis Zone
Sonic Riders: Digital Dimension
good choices
Not only are those great stages, but they remind me of Yugioh. Coincidence? Let's say no.