Sonic/Amy, Shadow/Amy, and Knuckles/Rouge are the only couples that really seem to have any degree of basis. Where the hell Tails/Cream came from, I'll never know.
Sonic/Amy is the obvious one of course. Though I don't believe Sonic will ever return Amy's love.
Shadow/Amy is relatively unlikely, but I can spot a few moments in SA2 that do sort of suggest that. Mainly, the big grin you can spot on Shadow's face when Amy mistakes him for Sonic.
Knuckles/Rouge was always something I kinda like, but like all good storyline hooks from the end of SA2, it was blatantly ignored, only being touched on again at the end of Heroes.
And before anyone comes screaming Vector/Vanilla, and Tails/Cosmo, Sonic X is not canon kthxbai.