Does the same guy from 10 different games count? (Ganondorf, if anyone's wondering). If not, then:
Ganondorf
Zant
Ghir (what I call Ghirahim)
Arbiter (Halo, but I don't even know if he counts since he turns good)
Dark Link
King Bulblin (TP)
man....most of the games I've played don't really have a set villain..... Moving on to the vague rather than the specific XD
Cerberus (ME trilogy, mainly last two games, kinda....you work for Cerberus in the 2nd game, but....)
Vex (Destiny....They're my favorite race to fight)
Subspace Emissary (The baddies in SSBB, including Bowser, Ganondorf, ROB (until they turn good), Master Hand, Tabuu, etc...the group rather than the individuals)
2nd through 12th place (in mario kart 8, anyways)