Sure why not. I won't include series where I've only played one game obviously.
Might and Magic - 6
This is always a tough one. I have a soft spot for MM1 but it does have serious flaws. WOX is awesome, but MM6's overworld and dungeon design is so good, and it's a series primarily about exploration, so I think it wins.
HoMM - 3
I love HOMM2, and in some ways I think its design is tighter (not to mention it looks and sounds the best), but HOMM3 has more content and a better engine, and ultimately I ended up playing it so much more than any of the other entries partly because of the random map generator.
Quake - 1
Half Life - 1
(not much of an accomplishment though)
Warcraft - 2
StarCraft - 1
Diablo - 1
TES - 2/3
Can't pick, Daggerfall and Morrowind are way too different in their ambitions, in fact almost polar opposites. I'd have loved a game with the strengths of each, but that's never going to happen.
NwN - MotB
SoZ is a close second. Neither of the main games on its own is worth much though.
SWKotOR - 2
Fallout - 1
DooM - 1
I like Doom 2's levels a lot, but the first game's had a simpler elegance that makes it superior IMO.
Blood - 1
Wizardry - 4
Ultima - 4
Heretic - 1
Hexen - 1
Thief - 1
Bioshock - 1
(not much of an accomplishment though, and I haven't even played Infinite)
Far Cry / Crysis - Far Cry 1
No contest, the games get exponentially worse as you go up.
Civilization - Civ 2
I think Civ 2 is the better game even though Civ 1 is the one I played most and still go back to.
Baldur's Gate - 2
I don't hate BG1 as much as some, and don't love BG2 as much as others, though.
IWD - 1
I still like the 2nd game though.
ME - 1
Dead Space - 1
(then again 2 is complete garbage and I didn't play 3, so not exactly a ringing endorsement)
Unreal - 1
Elite - 2
Dungeon Master - 1
Bard's Tale - 2
Borderlands - 1
(not a ringing endorsement considering how much 2 bored me)
Classic Gold Box - Pool of Radiance
Krynn Gold Box - Champions of Krynn
Savage Frontier - Gateway
Buck Rogers - 1
(huh only just noticed I always like the first one most in these)
Dark Sun - 1
Magic Candle - 1
Two Worlds - 1
Prince of Persia - 2
Original Mechner series obviously. This one was hard. I love POP1, and POP2 made me rage a LOT more, but I do think it's the better game overall, despite being incredibly hard in parts.
Tex Murphy - 4
First game is the most original, and I loved Tesla Effect, but Pandora Directive wins hands down, I think it's one of the best adventure games period.
Elvira - 1
Duke Nukem - ?
Really hard one there. I think both side scrollers are equally good, and DN3D is a great shooter, but best? I really don't know. I think I'd pick DN3D, but I'm also more of an FPS player than platformer.
Witchaven - 1
Gobliiins - 3
Another toughie. I like Gobliiins because it's the most original of the trilogy, but Goblins 3, despite (because?) being a more traditional adventure game, is the better one.
Myst - 1
I know most people like Riven more because it has more and tougher puzzles and is much bigger, but I find Myst to be tighter, more atmospheric and more enjoyable as a result.
STALKER - 1/3
Third game is more finished and better designed, and generally better on average, but the highest points in the series are all in the first game. Superb and unmatched atmosphere.
Ultima Underworld - 1
Gateway - 1
Spellcasting - 101
Monkey Island - 2
Dark Forces - 2
As in, Jedi Knight. Best level design in the series, and possibly some of the best in any FPS period.
Soldier of Fortune - 1
Not the greatest FPS but a lot of fun, and better than any of the sequels.
Leisure Suit Larry - 7
King's Quest - 6
Space Quest - 4
Police Quest - 1
Quest for Glory - ?
Gabriel Knight - 1
Dr Brain - 1
Phantasmagoria - 2
Shivers - 2
Warlords - 2
Ringworld - 2
Portal - 2
(mainly for the multiplayer, the SP of both games is pretty meh)
Eye of the Beholder - 1
Lands of Lore - 2
Despite the flaws I think LOL2 has some great level design, puzzles and exploration going for it, while LOL1 is a pedestrian blobber (though still fun)
Legend of Kyrandia - 1
Goddamn I've played too many games...
