I enjoy lurking on these types of threads, and this particular one didn't disappoint. I'll add my contribution to it, but I'll start with the following subcategories: Immersion, Tactics, and Lore.
My immersion top 3 are:
1. MOTB
2. Pillars of Eternity (I'm a sucker for the Watcher zoom-ins that were baked into it)
3. BGII
My tactics top 3 are:
1. TOEE (w/Circle of Eight mods...I couldn't play it otherwise).
2. Icewind Dale
3. Pillars of Eternity
My lore top 3 are:
1. Pillars of Eternity (I love the hard cover books, novellas, as well as the books within the game)
2. Icewind Dale
3. KOTOR
Overall top 3:
1. Pillars of Eternity. Backed the game, restarted it more times than I can count, love owning the physical books, love the story and the fact that we all own a bit of responsibility in helping to make it happen (from a monetary perspective). Yeah, clear winner for me.
2. KOTOR. I completed the game many years after its release, on a Mac port. I remember being completely blown away by the ending of the story, and all of the twists and turns along the way. I never completed the sequel of it, but I'm not ruling it out for another day down the line.
3. NWN. For the countless hours of play on a long since defunct persistent world (Mossbourne), for the many high quality mods that I played along the way, and for the absolutely stellar Aielund Saga that easily could have been an official release. It doesn't make my top three in any of the above areas, nut for nostalgia alone, it makes my top 3.
Of random note: I'm doing a simultaneous play through of Witcher 1 and Pillars, mainly Pillars for the last two days of gaming time. Witcher 1 has been absolutely stellar so far (I'm in Chapter 5 on my first play through), and I understand why that series is so revered. It'll probably be in my top 5 of favorites, once I'm done.
I have 2 and 3 also installed on my rig, as well as Tyranny. I would have been an early buyer of Tyranny, had it been able to run on my four year old Mac. Alas, it couldn't, and neither could most of the Witcher's (from a graphical standpoint)...so I recently bought an Acer gaming rig, which plays all of them very easily. My first Windows machine in over a decade (not counting those at work). I made that choice because I didn't want to lose out on being able to play POEII right away upon release.
Edit: various errors.