I'll name a few...

Krelian (Xenogears) - Awesome armchair villain who also dabbles in genetic engineering and scientific experiments on non willing human subjects hat may put Hojo to shame in just the sheer scale and different ways to make monsters out of men. His whole goal wipes out most of humanity and nearly ended the universe by trying to make contact with god. The crap he did to Ramsus alone makes him a glorious bastard among glorious bastards.

krelian.jpg

Id (Xenogears) - For those who want some mindless action, look no further than Id, whom every scene he appears in the game is both horrifying and awesome. Granted he's actually kinda easy when you get to fight him but in terms of cutscene powers the guy is a monster, and a total sociopath out to destroy everything.

Grahf (Xenogears) - I'm not a fan boy...Yes you are... but damn if Xenogears didn't have some of the best villains in a JRPG. Grahf is basically a mix of both Krelian and Id with a healthy dose of Darth Vader with DBZ powers just to give him flavor. His goal was to take over the main characters body so he could use both their awesome powers to kill god. I still know people with full body shivers if I utter his catch phrase "Do you want the power?".

Thanatos (Secret Of Mana) I have a thing for ancient evils possessing bodies of young men don't I? He was pretty awesome in SoM and really stood out among the Empire. He has an awesome final boss fight and a wicked boss battle theme... [WARNING SoM SPOILERS]

Sydney Losstarot (Vagrant Story) - Sure he's not really the main villain but he's definetly one of the best antagonists I've seen in a game. His mind screw on Ashley, his nasty summon powers and his awesome illusions made him a pretty unsettling figure to be charging after. This scene may have some MAJOR VAGRANT STORY SPOILERS, but it was the scene that just shows how badass this guy was.

Lavos (Chrono Trigger) - I usually don't go for "Forces of Nature" type villain, but the way Lavos works in Chrono Trigger's story and the mythos the games history is just spectacular. I take that back, it's because of Lavos that I don't care for Forces of Nature villains cause none have come remotely close to how awesome Lavos was. Not only the destroyer of three civilizations in the CT timeline, but even responsible for Human evolution and their ascent to being the dominant species all for the sake of his own evolution. Lavos never speaks and most of it's actions can simply be thought of either being against a highly evolved intellect beyond human comprehension or one of a baser being like a parasite. He's also the only boss who gets his own ending if he beats you...

I'll probably think of more but these are some of my top choices thus far.