Mortal Kombat 2 and Tekken 3 are the main ones for me. My brother and I wasted what must be weeks of time playing those things.
Street Fighter 2 I mostly played single-player, but I have many a fond memory. Plenty of not so fond ones too, as I could almost never beat Bison. I probably enjoyed Street Fighter 4 a bit more, as I was better at that game than 2.
MK DA was solid, as was MK vs DC (story/fatality issues aside). Those two don't really compare with MK9 and Injustice though. Brilliant games.
Honourable mentions (ie games I played a lot of but know they aren't at the top of my list):
Body Blows
IK+
Shadow Fighter
Rival Schools