Best Villain
 

I will start this off by saying this is for your opinion at said characters ability to combat the protagonist(s). This is not for who is your personal favorite. So if the villain has done things like, not immediatly killing the hero when able to, then you probably shouldn't put that person down.

Villain: Megatron
Series: Beast Wars
Pros: Incredibly cunning. He would anticipate his opponets tactics and counter act them. He cared nothing for morals and never fought fair. I was very impressed when I realized how much he thought ahead spoiler Trantulus (who was only concerned with himself) attempted to escape the planet since it was about to be destroyed. Knowing this Megatron created security holes so he could succed in getting a ship. But he left a virus in the programing so that it would fly into the weapon and destroy it. After removing all the safety devices of course./spoiler
Cons: Really his biggest problem was that about half of his group were plotting against him. But he only had so many soldiers so he couldn't just kill them.

Not a cartoon, but I'll throw this out there - the Cylons, from Battlestar Galactica.

I mean they basically won, right there in the first episode.

Yagami Light from DeathNote (although techniquely, the anime isn't done yet so I'm basing this on the manga) spoilers: Even though he loses in the end, it was because, ultimately, the protaganist was smarter than he was (and one of his minions F'ed up), not because he did something completely foolish (except yelling "I win" when he thought they were about to die). Must of what he did was brilliant (and insane, which makes him even better), plus he has the coolest 'bad guy glare' I've seen in a while.

*Oh, and Megatron from Beast Wars gets a runner up prize.

Thailog from Gargoyles.
If you've never seen the show then you would not know anything about him, but allow me to put it in the best way possible.
The main villain himself said that he had created a monster(Thailog). Thailog outsmarted him, overpowered Goliath(The main hero) and subsequently showed up in a few more episodes.

Sadly, the third season which was going to have him in it a lot, ended up becoming taken over by a new writing team that sucked suckifishly.

We Gargoyle fans have a rule Arlan; its called There was no third season and anyone who says otherwise needs to be hunted down and gutted like a fish. Although you're right, Thailog was a great villain, but since he didn't have much screen time it's hard to come to a definite conclusion about him.

Beast Wars Megatron is a good choice. But waht about Bertram, Stewie Griffin's half-brother? Nothing beats a swordfight in a playground!

Seconding the Cylons, mainly because 6 and Boomer are, as we say, teh sex. :P

Otherwise, I'm fond of Morganna from .hack//SIGN. All those mind games...yummy.

I wouldn't count Cylons because they are an entire race and we are discussing the abilities of one person.

Also winning doesn't mean you are best, it can mean your oponet just sucked or you had a huge advantage. One of the reasons I selected Megatron is because he was on equal footing with his enemies. If you look at most series the villain has a huge advantage and good guys still tend to win. My point is a good villain out thinks others around him and uses his abilities to their fullest.

I hate it when the bad guy is able to kill the protagonist from the start but doesn't. Or they have a massive army but only send one or two to attack when superior numbers would garentee victory

See that's what I liked about the Cylons. They totally had the drop on humanity, so what do they do? Slaughter us all, without warning, by way of the coordinated detonation of hundreds if not thousands of nuclear weapons put into place across a dozen worlds.

You know they're not fucking around, is what I'm trying to say.

Speaking of Gargoyles, I always liked Xanatos from Gargoyles, cause he was just so charmingly evil.

Good man.