If we go by most played (hard to pick a fave) I'd have to say fIGHTERS MEGAMiX or House Of The Dead for Sat. Or maybe Phantasy Star II for Genny. Or House Of The Dead 2 for DC. Hard to pick just one. Best game? Probably PDS for Sat. Very well done little epic they put together there.
Of course, I'm trying to think of just Sega titles - if we get into third party games too it's over. Too many sick games.
I'd say Mr Bones ! Though not perfect, it's the funniest game I've ever played. Maybe I'll add Golden Axe II on system32. Can't wait for the next version of modeler... There may be a release in 2 or 3 years :/