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>1, 2, 3, s&k, and cd
I'm still going to throw CD out there, motherfucker had quirky level designs, two good soundtracks, the introduction of one of the most memorable villains in the series, etc...
Still though, you basically eliminated all of the classic 2D ones. I'd say Adventure (1&2), Heroes, Rush Adventure, (fuck me if I had to pick a specific one of the Advance series games), Colors, Unleashed, Generations...
There, I just through out all the obvious ones.
Personally, I like 3D blast mainly because I'm a fan of isometric artwork, the music was great, and the bosses were actually challenging. Triple Trouble's also a relatively obscure title that deserves some more love... Secret Rings was okay... even though it's frustrating as shit at times. I'm personally hoping that SegaSonic the Hedgehog gets re-released (the trackball system could work wonders on a DS, 3DS, that one was a load of fun. Chronicles was a good title, proving that even Bioware can make sense out of the pile of fuck that is Sonic canon. X-Treme (with a bit of tweaking to run on the NiGHTS engine) is curious (you can find the files for it somewhere on Sonic Retro, I can't remember where though), but hell if I know if it had potential.
Just listing because I'm bad at picking favorites and making lists.