Colonel Jack T. Ripper (that movie’s just full of good names, though)
Reliant Robin (Mr Bean)
C’mon… Auric Goldfinger. There’s something disturbing about the “finger” part. And you can’t say the name without thinking of the Shirley Bassey vocal.
Possibly a bit obscure, but the names of most the characters in Stephen R. Donaldson’s Gap series are pretty awesome and match the characters to a T. The bad guys are:
Angus Thermopyle (starts as a bad guy)
Holt Fasner
Nick Succorso
Marc Vestabule (once human, now alien)
Even the good guys have great names:
Morn Hyland
Mikka Vasaczk
Warden Dios
Kiona Hannish
Sixten Vertigus
Dolph Ubikwe
Min Donner
And my favorite name of all…
Hashi Lebwohl
They might not sound like much, but like I said, the names match the characters exactly.
Simon Bar Sinister
I still like Dr. Evil. Make sure you call him Doctor. He didn’t go through 6 years of Evil Medical School to be called Mister, thank you.
Bad Horse, The Thoroughbred of Sin is an excellent #2.
It
Apophis
Call me old fashioned, but I think the traditionnal demons have hogged most of the evilest sounding names. You just know they’re in the wrong team.
Baal, Mammon, Belial, Azazel, Astaroth, Beelzebuth, Malphas, Andromalius… OK, I’ll put down the Goetia now, you get the point 
Hedley Lamarr - Blazing saddles. (thats hedley!!!)
Am I really the first to say “Pussy Galore”?
Not really evil just obnoxious, the guy from the movie Airport who indirectly causes the explosion by yelling: “grab that guy he’s got a bomb” Marcus Rathbone.
Solomon Grundy
Myxlplyx
Lord Farquad
James Moriarty
Voldemort.
Morgoth (sounds more evil than Melkor)
Ool and John Sunlight – both from Doc Savage books
Keyser Soze – I’ve never seen The usual Suspects, but that’s just a cool name.
RR
Archcount Obdrath von Lucifuge (Starslip Crisis)
Jean-Baptiste Emanuel Zorg
Flat Top.
That’s Professor James Moriarty to you. And don’t forget his brother, who… er, um, has the same name.
I’d add:
Charles Augustus Milverton
Shelob
Sir Meliagrant
Morgana le Fay
Darth Sidious