FlintlockJazz: I don't know anything about this, but if they were doing it for free and making absolutely no profit from it then no, Sega cannot do absolutely anything to them, and to attempt to do anything to them would make them look like utter dickheads and ruin what's left of their PR for Sonic. Otherwise you would never see any fanfics being written, or artwork being made of famous characters since that's pretty much the same thing.
Roberttitus: May I direct you attention to....
http://en.wikipedia.org/wiki/Chrono_Resurrection You are reffering to Square Enix there, the tyrannical approach they have to fan made projects is world famous.
I don't see Sega doing an anything here, since full flash sonic games are plastered all over the net without a peep coming from sega as to their legality. Also, as flintlock states the amount of sonic fan fic would elicit a response by sega. Yet they have let it continue unabated, even the heavily erotic ones.