Yeah man, there are some classics mentioned in here

All forms of ridley were fun as hell (basic, neo and mecha) and kraid obviously.

Metal sonic from sonic cd, knuckles from s&k and the final bosses from sonic3 plus knuckles.

U.Rugal and S.akuma from capcom snk are mean machines, love em. Bison from SFA3 was awesome too.

From the final fantasy series i pretty much loved to fight anything that was a summon. Bahamut being the best in most cases.
All time favorite FF bosses are shinryu omega and neo x-death, for supreme awesomeness and Gilgamesh obviously for being damn right cool. Other memorable fights include Necrophobe, Atamos, archeoavis from FFV, cerberas, omega weapon and griever from FFVIII and emerald from FFVII.

Mentioned somewhere above is Mewtwo. I usually catch him pretty quick with ultra balls and once (hell yeah) i caught him with a single ultra ball (fire red version) But the legendary birds were fantastic fights and especially the legendary dogs. Not to mention lugia.

The nemesis from resy evil 3 absolute owns too.