Ethan Rayne! He was the quintessential Buffy villain: snarky, smart and totally nuts. Seeing more of him and Giles backstory would have been awesome, too. Maybe a flashback or an alternative reality episode.
Angelus was of course a great big bad, and its not the ridiculous amount of love I have for Angel. He took no prisoners, he never relented, and best villain quality of all: he got in to the nifty gritty of Buffy's psyche and tore it apart. They should have done an Angel/Buffy crossover from when Angelus came back later on. Seeing him interact with an older more mature Buffy would have been so interesting to see.