Oh god, so many to choose from, but I'll try to narrow some down.
Kefkas theme instantly came to mind when I read the thread title. THIS is one of the best examples EVER of how to do a villains theme. I rank it higher than pretty much any other villain theme in history. This leitmotif perfectly captures the insanity, destructive nature, and down right horrifying yet glorious essence that is Kefka. It still sends shivers down my spine and perfectly captures his progression from an annoying buffoon, to the nihilistic and maniacal all powerful threat he becomes.
Oh and I can't forget the Orchestrated version. It's a little different, but still the same vibe overall. It will sends shivers down your spine, and instill real fear.
Magus' theme from Chrono Trigger is another instant classic. The dark and foreboding nature along with the epic and menacing follow up is really effective. And the Celtic vibe goes well with the setting and 'dark wizard' motif.