Well,I have quite the list.
Web Animation
-The Auditor (Madness Combat) He's smart. He's powerful. He's the ultimate bad guy.
-The Meta (Red vs. Blue) Again,intelligent. Powerful. Watching it at work is VERY satisfying (especially during Monty Oum's animated sequences). And...I enjoy it's thought process.
-Agent Washington (Red vs. Blue) He's pretty much the opposite of the other two. He's perfectly normal,if a bit unhinged. Also induces laserface.
Books
-Opal Koboi (Every other Artemis Fowl book) She's smart,she's insane,she has NO concept of mercy or remorse. If she got past her God Complex,she'd be unstoppable.
-Artemis Fowl II (The first Artemis Fowl book) He's a genius,and had the perfect plan. If Juliet kept her shades on,and didn't drop the radio,the plan would have gone off without a hitch.
-Paul Grayson (Mass Effect Ascention) He's a terrorist,murderer,drug addict. And loving father to a young autistic girl. Seriously,I felt for the guy.
Games
-You. Yes,you! (Dungeon Keeper) Yes,you're the bad guy in Dungeon Keeper. Any questions?
-Kane (Command & Concuer Tiberium series) He has a plan for EVERYTHING. Nothing is a setback;every victory,loss,and disaster is another step forward for this man,somehow. Also,apparently,he's the Biblical Cain. Trippy.
-Lloyd (The Legend of Dragoon) He's a member of a supposedly extinct race,and is a very talented swordsman. He is very fast,and is always a step and a half ahead of you. Why is he a bad guy? He wants to help improve the planet.
Film
-Korso (Titan A.E.) The man has a cool ship,an awesome crew...And he pulled the wool over everyone's eyes for most of the movie. Then he had an awesome moment.
-Preed (Titan A.E.) Same deal as Korso,but he lacks any sort of concience. Makes him an amusing guy,actually...
-Daemon (ReBoot

aemon Rising) She is the ultimate virus. She had successfuly brainwashed every program in online system on Earth,except Bob and Hexidecimal. Her plan ULTIMATELY SUCCEEDED. Then the HexVaccine hit.
TV
-Blokk (Shadow Raiders/War Planets) He's completely indestructible by conventional means. He literaly has the touch of death. Usualy,he's a complete idiot who preffers brute force. Unless you piss him off. Then he becomes very intelligent. And nearly succeeds in killing off every major character. On his own. Plus,his accent is awesome.
-Megabyte (ReBoot) Smart,strong,head of a massive viral empire in Mainframe...He's pretty good. But Bob's better.
-Newton's Laws (MythBusters) Any questions?