Keyboard/mouse controls have improved since those days. Sure, you still get some games that have way too many functions bound to way too many keys, but that's mostly a design flaw with the game itself. Good games have sufficiently streamlined their controls to the point that I can do everything important on the keyboard without even looking at it. The mouse is also a lot more precise than an analog stick. That's not a dig at gamepads either--I use the 360 gamepad even for some PC games--but for anything that involves pointing and shooting, the mouse beats the analog stick hands down, at least in my experience. I remember a big uproar over some FPS on the consoles that someone had modded their console to play with a keyboard and mouse, in fact. He was accused of cheating because it was so much easier for him to aim than it was for his gamepad brethren.
Then again, when you've got a platformer like Prince of Persia or Tomb Raider, the mouse and keyboard can be pretty awkward. So, really, it's the game that decides what controller is best for me. Anything with a first-person perspective: mouse/keyboard. Anything where you're primarily moving around instead of pointing and shooting: gamepad.
But back to F3: Anyone kill Three Dog? I just read about what happens if you do and I'm totally doing it on my next game.