Doom: Straight port... N64 controller or Mouse & Keyboard? I'll take the latter.
Turok 2: My god man what are you smoking? It had some of the clunkiest controls and their resulting movements known to man!
Duke Nukem: As in Duke Nukem 3D port or as in Duke Nukem: Zero Hour? If it's the first then I'll gladly refer you to what I said about Doom 64, if it's the latter then I'll refer you to what I said about Turok 2 (but obviously with a hellovalot less emphasis).
I remember the first time I played Turok 2. First I chose a tank character and decided he was too slow so my friends said to choose a lighter character if I preferred a more agile and responsive playing style. Having done this and not noticed the slightest bit of difference I vowed never to play the game again...
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I, unlike most people seem to be, am not a kboard&mouse whore :p I will full well play an FPS with a controller, I see nothing wrong with it. Hell, I played TFC for about 18 months with a joystick and keyboard and did fairly decent. When I finally decided to try a mouse, my skill plumetted to the ground since I was not used to it.
I never noticed anything wrong with the turok controls, both my brother and I considered them the best console FPS control setup untill Halo came along. Last month I just replayed through the entire game and didn't feel the controls were bad. When I first started it was a bit akward but I think only because I hadn't used an N64 controller in awhile, by the second level I was doing just fine. I also speak of turok singleplayer, multiplayer was not that great and we didn't play it often. (not to mention if 2 or more people fired the Firestorm Cannon the system would lock up :p)
Never played Zero Hour, only watched my brother play it. However the original was great fun with multiplayer, we would sit for hours on end playing it.
Oh and a final comment I have on the mouse/controller FPS debate, I will stand by this argument forever that controllers/joysticks are ten thousand times better at tracking moving targets with sniper rifles or other such things. You just
can't steadily track with a mouse.