Cause I'm getting confused as to which I used to watch ... I swore it was Adventures of Sonic The Hedgehog - just the name rings bells in my head ...
"The only thing Bond will be fighting is HIV" - Frankie Boyle, Mock The Week.
I believe that in AoSTH, the Freedom Fighters (Sally, Bunne, Rotor, etc.) don't exist. It's just Sonic and Tails. The animation is also more, for lack of a better word, kiddish. It's mainly a comedy relief series. (I vaugely remember that some episodes ended with a 'Sonic Says' segment, in which Sonic and Tails come on to preach a Daily Lesson to children, i.e. memorize your address in case you get lost, steeling is wrong, etc.)
Sonic the Hedgehog, on the other hand, is a little more darker, and more serious.
http://www.fanfiction.net/~datagirl3
This has Sonic teaming up with Princess Sally (the chipmunk/squirrel), Bunnie, Rotor (Walrus) and Antoine (the coward) fighting to destroy Robotnik's plans in Robotropolis (his polluted city that he took over from).
AoSTH is the one with Scratch, Grounder and Coconuts in it. Every episode had a Sonic Sez at the end, some now considered legendary (sexual harassment, booze, smoking).
If you are at the UK (like myself), most likely you have seen the below one more often but to make things even more complicated Channel 4, TCC (and recently POP) refer both of these as just one series (aka Sonic the Hedgehog). Oh and TCC often swapped the intros of the shows around to make it even more confusing.