Don't much like the new master, although that might be more the fault of Russel Davies than anything. I don't like how he is clearly deranged in the new series and they made up the whole sound of drums thing because he wasn't like that originally. He isn't really full of loathing and hatred like Vader is either- and certainly isn't as much of a badass. Although stealing Nyssa's dad's body was a pretty dick move.
Another candidate for best bad guy is A.M. from the short story 'I have no mouth and I must scream' because of its pure despise and malevolence towards humans.
"HATE. LET ME TELL YOU HOW MUCH I'VE COME TO HATE YOU SINCE I BEGAN TO LIVE. THERE ARE 387.44 MILLION MILES OF PRINTED CIRCUITS IN WAFER THIN LAYERS THAT FILL MY COMPLEX. IF THE WORD HATE WAS ENGRAVED ON EACH NANOANGSTROM OF THOSE HUNDREDS OF MILLIONS OF MILES IT WOULD NOT EQUAL ONE ONE-BILLIONTH OF THE HATE I FEEL FOR HUMANS AT THIS MICRO-INSTANT FOR YOU. HATE. HATE."
Pretty fucked up story, worth reading if you haven't

Also Dr Claw from Inspector Gadget is a good villain:

The deep raspy voice, the gauntlet, and never seeing his face (gives a similar air of mystery as Vader does under his helmet) make him a badass in my book. And that fucking cat.