There's plenty of baddies in anime, so here's my own personal list from the P.O.V. from an oldschool otaku:
10. COUNT CAGLIOSTRO (Lupin The 3rd-Castle Of Cagliostro)
This dude is in there just because he fills the part of the stereotypical mustache-twirling jerk so well. He rules over his country with an iron fist in a way that'd make Dr. Doom proud. Plus, he's such a sneering self-absorbed pedophile, you almost have to accept that as meritable. You'd think the nations of the world would've realized that he's evil simply by the way he dressed up like a supervillain at his own wedding!
9. CAPTAIN GINYU (Dragonball Z)
While most dudes would vote for Frieza or Cell as their fave DBZ @$$hole, the head of the Ginyu Force wins points for totally puting down Goku. He leads Frieza's main assassin squad, and makes them out to bne like they're a team of superheroes by doing Power Rangers poses. Ginyu can switch bodies, which he does with Goku after he wounds himself and takes over his near-Super Saiyan self. Too bad he ends up as a frog.
8. JOKER (R.O.D. The TV)
While as in the original Read Or Die OVA series he seems like he's the main leader of the good guys(the British Library), in the TV sequal its revealed that they only reason they were trying to save the world in the first place is so they can take it over themselves. Joker is a manipulative, deceptive, slimy bastard who uses his position to slowly advance the British Library from not only taking over the world, but completely altering reality to their whims.
7. TEAM ROCKET (Pokemon)
These guys are here purely for tenacity. While chasing their prey far beyond the point that Wile E. Coyote would've given up on, Jesse and James have continued to chase the dorkiest kid in anime and his freakishly-large rat for over 12 seasons. While using every disquise in the book, and digging more holes than in every golf course in the country, they just won't give up! That's at least worth a merit badge.
6. SOSUKE AIZEN (Bleach)
While I'm not the biggest fan of Bleach, this sonovabitch totally made an impression. Aizen starts out seeming like the nicest guy in the Soul Society, but gets brutally murdered. Turns out he faked his own death, kills his loving subordinate, and grabs the ultimate power in the afterworld. Aizen then descends to the world of the hollows(evil spirits), and takes them over. He creates vast illusions to have his enemies fight among themselves to lead them away from him obtaining his goals. Very dangerous!
5. DR. HELL (Mazinger Z)
The original anime mad scientist! Before Dr. Wily, Dr. Hell was the first creator of evil robots. He stole the technology to make monster mecha from some ancient Greek ruins(they had giant robots back then?), and then makes a secret island fortress to house his army. He keeps trying to destroy the super robot, Mazinger Z, but keeps failing to do so. Then he apparently dies, but comes back to fight the more upgraded Great Mazinger in the most powerful robot yet. The story then reboots him in the Mazinkaiser anime, but more like an even more vile version from the original series. Known as Dr. Demon from Tranzor Z, Doc H. is on seriously sinister antagonist.
4. KAGATO (Tenchi Muyo)
Another evil scientist-type, this schmuck was a student of the self-proclaimed greatest genius in the universe, Washu. However, he was clever enough to trap her for over five thousand years, and take control of her daughter to ravage the galaxy in his search for universal power. Kagato then brings his awesome battleship to Earth and torments Tenchi and the other girls. It's later revealed that he was originally a hermaphrodite, which is where his hatred of women came from, although he removed the female part of himself. In the Tenchi Universe TV series, Kagato was even more deceptive by posing as the lost hero Yosho, subsequently taking over the galaxy and turning the show's heroes into fugitives. This guy could give Lex Luthor lessons on being an evil mastermind!
3. JINNAI (El-Hazard)
This laughing jerkwad is the biggest oppurtunist ever! He first cons his way into being the class president, but when his position is threatened he tries to kill his opposition. The two of them end of going to the magic world of El-Hazard where Jinnai gains the power to communicate and influence the might race of insect creatures called the Bugrom. Along with the slinky Queen Diva, Jinnai establishes himself as the main conqueror of the Bugrom Empire. He comes a little close once or twice, even gaining control of the powerful Demon God, Ifurita. Jinnai's megalomania is very commendable as a villain, and while he'd not be the kind of guy you'd want to be in back of in homeroom, he's someone you'd want planning an assault on a neighboring kingdom.
2. MEGATRON (Transformers)
First of all, YES, Transformers is an anime! Megatron is the Grand Poobah of the Decepticons, with plans to not only conquer their homeworld of Cybertron, but the whole universe! He's a master strategist, and one of the most calculating villains ever. Aside from his cole demeanour, he also has a sense of honor, and despite his want to destroy his archenemy, Optimus Prime, he respects him as a worthy advisory. He also cares for the future of his fellow Decepticons(aside from maybe Starscream), so he isn't just in the galactic domination thing for himself. Most other versions of Megatron like from the Transformers movies have him being more vicious, where as in other shows like Beast Wars they have him as being a real menacing the very fabric of reality. Megs is as close to Darth Vader as you'll find in anime!
1. PRINCE LOTOR (Voltron)
Now we're talking "hyperspace"! Lotor is a pimp of epic magnitude. He's everything a young horny aspiring up-and-coming bad guy would want to become. First off, he commands a nearly endless armada of starships and giant monsters, and takes any chance he can to usurp his father's place on the throne. He's also a play-ah! If he's not trying to take down Voltron, Lotor surrounds himself with hot chicks, and is willing to commit intergalactic war just to tap some princess booty. By serving his inner-neanderthal, Lotor balances his passions for power and glory while laying waste to whole planets in his quest to go further than Darkseid ever dream of. Lotor is keeping his galactic-dominating pimp hand strong(even as a cyborg)!