The most notable ones for me are of course the site for Sonic Robo Blast 2 (est. 1998) and Sonic Retro (2004). I guess what site is considered 'old' is subjective. SonicSCANF is a Russian Sonic fansite that's still running, and it started in 2008. Sonic Fan Games HQ is also still active, although as a forum only. I miss when it had spritesheets and a page full of fan games. Caiman.us hosts a lot of old fan games and usually has links to the homepages of them.
I know most of the sites hosted by emulationzone.org are still up, such as the Gregorsoft site (
http://fanmade.emulationzone.org/gregorsoft/frames.htm). The fact that place and all its hosted sites is still up really warms my heart; somebody, presumably one of the admins, has been keeping the site up for over a decade despite its inactivity.