Like Satan said (forgive me, Jesus), there are different categories of RPGs, and I don't think I'm well-versed enough to go beyond WesternRPGs and JRPGs (even then I may be off with what I lump into those categories).
As far as JRPGs go, I have very few under my belt. Very few. As a genre, they don't appeal to me, largely because they (seem to) revolve around established characters with defined motives, and the role-play element mainly consists of character builds and customisation (which, to me, makes them no different to most other third-person action games and not exactly RPGs, but I won't argue the point).
To that effect, my pick for best JRPG would be the only one I've ever played and liked: Paper Mario: The Thousand-Year Door.
Simply put, it charmed the crap the out of me and came along at pretty much the exact right time for me to enjoy it. I had a lot of fun with the style aspect of the combat, the music was great, and it had many memorable chapters. On reflection, the game has a lot of problems, but don't they all?
I could never get into the original Paper Mario, though. I'm not sure why. Every time I try it, I get to the desert and then lose all interest.
As far as WesternRPGs go I'm a lot more experienced (but still not as much as I'd like to be — I'm currently playing through a pile of isometric RPGs and having a great time with them). I desperately want to gush about Vampire: The Masquerade - Bloodlines because it's a cracked diamond and an absolute testament to how writing, atmosphere, and world-building can save a game.
But I can't say anything other than Morrowind. Anything else would be a lie.
The essence of an RPG, for me, is choice. The character is mine, one I have created, one whose story I will write. Start with a world, flesh it out, give it history, give it culture, give it rules. Then, give me a character editor and an introduction that allows me to determine my background. Then plonk me in that world and kindly eff-off. Choice and the ability to write my own story. That is an RPG to me, and nothing I have ever played has held true to that quite like Morrowind does.
It's flawed, I'll never shy away from that, but the absolute freedom to do and be whatever I want, to define what experience I have on my own terms, trumps all of the issues for me. I have spent more time in Morrowind than any other game ever. It's not even a close contest. Second place would be thousands of hours behind. I've lived more lives in Morrowind than I can recall, I've been everything from a raging barbarian to an apolitical scholar, a travelling merchant to Walter White (a friend and I decided to find the recipe for skooma — which, it turns out, is impossible to make without cheats — and started as wimpy alchemist nerds and eventually ended up as Dons of a very lucrative drug trade across Vvardenfell).
This game defined what an RPG is to me and it will always be dear to my heart, no matter how hard Todd Howard tries to make me hate the franchise.