Alright, folks, if you haven't played KotOR2 and ever intend to (and you really, really should), don't read this. Too many spoilers.
I am a big fan of the Knights of the Old Republic games. They manage to flawlessly combine fan-made Star Wars (fuck Lucas--anyone who has ever read Timothy Zahn's books knows this is the best, most carefully detailed version of the SW galaxy) with the RPG genre. They've got an awesome setting (naturally), great plots, and better characters. They've got more realistic and gripping backstories and personalities than most other RPGs, and it can be hard not to like even the ones with a heart as black as Darth Vader.
Case in point for me would be Kreia. Now, I do not personally LIKE Kreia. If you've played the game, you'll know that she's not exactly the nicest or most moral person you'll ever come across. She's vicious, manipulative, and she bullies poor Atton all the time (I love Atton). She's Machiavellian to an extreme, just a bit crazy, and at least as much a servant to the Dark Side as she isn't.
But man, as a villain, Kreia is the best I've ever seen in an RPG, plain and simple.
Point One: She's tough. She's genuinely powerful. She's a master of the Force like few others, knowing its ways and using them to her advantage. She can use a lightsaber, which automatically makes her more of a force to be reckoned with than any villain using a regular weapon. She can take a hit (and by a hit, I mean have her hand cut off) and keep on truckin'. She doesn't NEED to do some quest for magic objects to give her the powers of a god. She's smart enough to set the fall for anyone who opposes her without resorting to one-winged angel crap like that. When you deal with Kreia, you deal with someone who's not going to futz around with that nonsense--she'll just either kill you, or, more likely, let you live to unwittingly do her bidding. If Kreia decides to let you live, it's not because she's being a stupid FF villain who doesn't have the good sense to kill protagonists after whupping them early in the game while their levels are low. It's because she knows she WILL make use of you, and can probably do so while making you mentally suffer.
Point Two: The game gives you ample opportunity to know Kreia. Like, KNOW Kreia. This isn't like knowing, say, Seymour of FF10. With Seymour, you know the very, very broad and general (not to mention really dumb) reasons for his villainous actions. This is true of most villains in RPGs, even the good ones--you just don't get too really involved in understanding them. A few, however, like Fou-Lu of Breath of Fire 4 or Orsted of Live-A-Live, are evil characters that you're given a really good amount of insight about, both in their personalities and the reason they do the evil things they do. Kreia, however, blows these two away. She hangs with your party for most of the game, and in that time she tells you all about herself. Her past, her ideals, the qualities she admires and the qualities she despises, her understandings of people and the ways of the universe, and eventually how and why she set everything up. Kreia is a realistic human being in a way that few characters (and of those few, just about no villains) in games are, complex in dozens of different ways that intertwine with each other. Even in a game series with such strongly defined personalities as KotOR2, she really stands out as a character whose creation and development are extraordinarily solid and deep. Folks, a great many of the classic works of literature I've read in my time at college as an English major don't have characters of this high a quality.
Point Three: The voice acting for Kreia is pretty much perfect. Not a big deal, I know, but still, when most of the game's more insightful and thought-provoking content comes from her, it really helps that it's delivered by a voice actress who can get just the right inflections of aged, dark wisdom to match Kreia's personality and words.
Point Four: Kreia wins. Everything. She's the most successful villain of any RPG ever, because she accomplishes every single goal she has. Kill off the remaining survivors of the old Jedi order? Check. Revenge on the Sith Lords who betrayed her? Check (no easy task, either--one regenerates all wounds done him, and the other one is such an unnatural horror that he could very likely defeat every single normal Jedi who ever lived--Yoda, Palpatine, Vader, Luke, EVERYONE). Set the stage for several new Jedi, who know what it is to be human first and foremost and Jedi after that, to create a new order which has a chance not to make all the mistakes the old one did? Check. Bring some balance to the force? All of the above work towards this one. Help prepare the galaxy for the inevitable and fast-approaching day when the Sith finally strike? Check. Send Revan a powerful ally to aid him in fighting the Sith on their own turf? Check. Just about no major move of the Light Side or Dark Side in this game is made without Kreia's making sure it works to further her goals. I mean, even when you kill her at the end of the game, you're STILL doing exactly what she wants--one of her goals is to train her greatest apprentice of all, and that apprentice having the strength of body, Force, and will to kill her will be the way to prove that she has succeeded, her final triumph. How many villains can you think of for whom their final defeat (not just I'm-Dying-But-Not-Really, like Seymour) is an essential part of their plan? Not many.
Point Five: You identify with Kreia. Understanding her isn't just a case of knowing where she's coming from, it's also a case of empathizing with her at times, acknowledging that there's wisdom in her ways regardless of whether they're good or evil. Villains aren't characters you can very often really connect with, and if they are, then you probably have a few issues. Kreia, though, you could argue the merits and weaknesses of her philosophies and insights on humanity, society, karma, and life for hours on end.
In the end, there's really no villain crafted with quite as much care and expertise as Kreia is. Buggy and unfinished as KotOR2 may be, the presence of a villain of Kreia's caliber alone makes it a great RPG.