Best antagonist?

I've already seen the top 3 characters list, but I'd prefer to narrow it down to just antagonists, try and post interesting villains or just amazing and funny villains. (Lets try and avoid posting Sephiroth please :P)

My favorite; Emperor Mateus from FFII



Reason: You fight your way to his palace, fight his best men and kill him, only to find he resurrected himself, killed Satan when he came to take his soul and took over hell. Then, when you thought that wasn't enough, he split his soul in two so that the other half could kill god and rule heaven.

GLaDOS (Portal series),
G-Man (half-life series), and
President John Henry Eden (Fallout 3).

now this is fun.
Emelious from Grandia 3
Wesker from the Resident Evil series
Seymour from final fantasy 10

Fuck. Then i say

Shao Kahn from the Mortal Kombat series and The Joker from the Batman series.

Dead master

I love the batshit crazy villans so im gonna go with my top 3 being

Juri-Streetfighter

Kefka-Final Fantasy 6

Andrew Ryan-Bioshock

Honorable mention:pyramid Head-Silent Hill

Mr. Scratch from Alan Wake.

Count Dracula. Duh.

Gilgamesh(Final Fantasy V)
General RAAM(Gears of War)
Giovanni(Pokemon)

Vladimir Makarov - MW3

Sun Li aka The Glorious Strategist from Jade Empire. Any reasons I could give would be considered a spoiler. Actually, even listing him here is pretty much a spoiler in itself...

Or Vladimir Lem from Max Payne 2.

Darth Malak from Knights of the old republic 1.

He's one of these antagonists that made me think quite a bit on, what was my characters position in the game world and how to affect it.. How my decisions lead from one point to another.

Simply from that, he's one of my personal favorite antagonists.

Akuma
Wesker
Bigboss (First Metal Gear)

SHODAN - System Shock 2

AM - I Have No Mouth and I Must Scream

GLaDOS - Portal

Evil AIs make such awesome bad guys.

you sir, are god

BIG BOSS from the Metal Gear Series nuff said

Plenty of good suggestions, but how the fuck has no-one mentioned Ganon?

Just like the original Deus Ex, I've reinstalled System Shock 2 on my desktop more times than I care to count.

Grahf from Xenogears.