Adventure 2 is still my favorite, although my brain might be riding on Gamecube birthday memories. I've played it recently and I still like everything about that game. The treasure hunting was kind of annoying, but still fun. Sonic/Shadow levels are great. Second is Generations. Awesome game all around. Was kind of hoping for some Sonic Adventure 2 style online racing mutliplayer, but eh. Leaderboards are good enough. Third is Colors. I like that game. Kinda hated the controls and level design at times, but I still like it. Forth is Secret Rings. Bought a Wii for that game. Shit got real once you upgraded Sonic. Fifth is Adventure 1. Haven't played it in a long time, but I have fond memories of Sonic's storyline.
Sixth is Unleashed. Daytime stages were perfect imo. Sadly, everything else about the game was ass. I'd love a game that had only Unleashed day-type stages with its controls. It would be my personal favorite Sonic game. Generations and Colors doesn't feel like Unleashed daytime to me. They are close, but not good enough. Colors was kind of restricting, and Generations is all over the place with its Modern Sonic level design. Also, I prefer the controls in Unleashed HD daytime compared to Colors and Generations. Infinite Drifting and QSS all day man.
Is it weird that I think the Wii version of Unleashed is the better game overall? Ignoring the Werehog because he's shit in both versions, I thought the Wii version's daytime stages were still ok and I preferred Holoska and Eggmanland in the Wii version. Also, Wii version did boss battles better and had no stupid medal collecting and it only took you seconds to get to levels instead of walking around a hub like in the HD version.
Heroes is in seventh. I thought it was ass, but above the remaining three. I had some fun with Team Sonic on the first time through, but the bad controls and glitches and dumb level design fuck that game up. I'll put Shadow in 8th place. It's bad, but not Sonic 2006 type bad. It's still playable at least, but I don't see why anyone would want to play it.
Black Knight is ninth for me. That game was letdown total. How do you take Secret Rings and make all the little stuff better (in game menus, graphics, music, and story), but make the gameplay worse? Fuck that game. Should have been an open-world, faster Zelda rip-off that let you used a controller instead of the Wii remote. Game would have probably been decent with better level design as well. I'd still take it over Sonic 2006 though.
List
Good:
Adventure 2
Generations
Colors
Secret Rings
Adventure 1
Average:
Unleashed
Heroes
Bad:
Shadow
Black Knight
Sonic 2006
Not well versed in handheld Sonic titles. I loved Rush 1 and Advance 1 + 2, but don't really care for the others. Also, Sonic Battle was amazing.