I make no guarantee of these Sonic stories being any good, I haven't read them in so long, and well, we all know how a story can be very different after so many years. But these are the ones I remember reading and enjoying when I was younger.
Sonic Stories by Robert Brown and Francis Tolbert
I think one of them quit the team and the other made a new account on FF.net and is continuing the series, but I can't remember exactly. Also, just so you know, quite a few OC's get created during this series. I think one of them is a little gary-stuish, but not horribly. Like I said, been awhile. Regardless of the OC's, main focus is still on the SatAM characters.
Netraptors Site
Another source of Sonic fanfiction I read when I was a kid. A lot of it is back from the day before FF.net became the dominant website for fanfiction, so I remember a few gems being collected there, but can't remember what exactly. It has it's own search function, so have fun. If I were to recommend anything, it would be Netraptors own fanfiction. Same rules apply as Robert and Francis's stuff though, been a while. Also several OC's throughout the series. Just get by the introduction of Slasher, who's a bit of an SI/Macguffin, but not horribly so. If memory serves right.