Lavos did it first and Lavos did it better

I think Xenogears had some amazing villains, honestly. Ramsus, Grahf, Krelian, Miang - pick whomever and you won't be disappointed.

And then you can't help but love some of the FF villains - Golbez was cool due to that thing by the end which kinda turned everything on its head, Exdeath was deliciously hammy, and then people like Kefka and Kuja are just way too fun yet reprehensible at the same time.

Nyarlathotep from the Persona series is also pretty friggin' great, if you ask me, to the point that many fans are actually looking for traces of his presence in the new games. Other than that, though, SMT doesn't really have memorable villains. There are a lot of villains, but aside from YHWH, there isn't really one central villain in the games, and YHWH may be the most evil villain in RPG history, but he's not exactly the most developed character, more relying on his connection to the real world and expectations people have of him.

Pillars of Eternity had a pretty weak villain, IMO, but Baldur's Gate had Sarevok, who was cool. Although, technically, I didn't really care much for him either until the expansion to II when (SPOILER)he made a heel-face turn.

And I love Fawful from Bowser's Inside Story. A freaky green dude that just keeps talking in hilariously broken English is all kinds of fun.