I won't include any games that I haven't played, so this list won't be entirely objective.
[sub]But you knew that already.[/sub]
Best:
1. Baldur's Gate 2. Improves upon the first game in every way, and features a rich, complex plot. The gameplay is a little stodgy due to it adhering to AD&D rules, but it's great fun once you get the hang of it. I may be a little biased since I've been playing and re-playing this game since I was.. twelve? Something like that.
2. Persona 4. If you took the elements of this game out of context and suggested them as game ideas, I'd probably call you an idiot. Or at least I would have done that, before I played Persona 4. Let me be clear about something: I hate VNs, I don't get dating sims, and I quite often find myself disliking people in general. Despite this, I love Persona 4 [small](and 3, but it has too many problems to be included on my list)[/small]. Everything in this game just works. Not just in gameplay, but philosophically and psychologically. Everything.
3. Dragon Age 2. Yeah, ************. My actual #3 is Mass Effect 1[footnote]Or Chrono Trigger, or Planescape: Torment or Jade Empire, or Tales of Vesperia, or Final Fantasy IX. To be honest, I just had a hard time deciding.[/footnote], but I figured I'd throw you a curveball. Don't get me wrong, I understand the criticisms made against this game. The gameplay didn't need to be simplified, and a lot of enemies and locales are directly copypasted.
That said, it's amazing. There's moral ambiguity occasionally bordering on nihilism here, as well as all the other things I miss whenever I play a JRPG: Violence, politics, intrigue, conspiracies, race, ideology, lesbians. The entire story hinges on the struggle between the chantry and the circle, and actually studies the implications and effects of all the fantasy elements introduced in Origins. Now all they need to do is release an expansion where you play as Merill, and I'll gladly sell my soul to the EA devil.
Worst:
1. Risen. Christ. This game is why I'm skeptical to any WRPG not developed in an English-speaking country.[footnote]Fable is why I am skeptical to any WRPG developed in an English-speaking country[/footnote] A completely broken combat system, samey enemies, a terrible leveling system (you pay gold for skills that you've ostensibly already learned? Why, that makes sense!) and no plot. None worth following, mind you.
2. FFXIII. I have defended this game before, and it really isn't as bad as everyone says it is.
However, it's still pretty bad, and it has some really shitty writing.
3. Oblivion. What's that? I get to wander around an incredibly boring landscape for no reason, going through identical dungeons and caves fighting enemies that are always my level? Wait, is the leveling system broken too? Does it work more smoothly if you actively subvert central aspects of the gameplay? Well, SIGN ME THE FUCK UP.