I'd have to go with Virtua Fighter. I have so much love for the series.
Unlike other fighting franchises, I find Virtua Fighter to be so pure. It's hard to explain. I guess it feels very stripped down to the bare essentials, but because of this it just feels so perfect. No insane story mode, no over the top kills (in fact, nobody dies), no super crazy combos. I find that even when there is a longer combo, it makes sense in terms of the whole combination of presses translated to the execution.
Even as the series progressed, it hasn't lots its way. Everything is still lean and simplistic, but everything has gained a greater depth. It really is what it says it is: a virtual fighter. Not something stupid like Legends Tournament Fighters Apocalypse.
So having said all that, I'd have to say my favorite SEGA fighting game is Virtua Fighter 2 for the Saturn, with Fighters Megamix as runner up. Megamix, mainly because it takes what I love about Fighting Vipers and Virtua Fighter and crams them into one game, plus tosses in a lot of AM2 fan service.