I do that a lot... I am forced to bring my laptop to school, so I load up Counter-Strike and some other games to play in class. Shh.

Yuck, thats like playing an RTS with a controller! Just... wrong...

Some mappings depend on the functions each game has, but my typical setup looks like this:
Movement: WASD (strafing on AD).
Reload: R
Use/Enter/Exit: E
Jump: Space
Crouch: Left shift
Switch weapon: Mousewheel
Primary fire: LMB
Secondary fire/zoom: RMB
Mouselook: On (I'm guessing everyone uses this)
Invert Y-axis: On
If a game has both walking and running, or running and sprinting, I map the faster option to left shift, and move crouch to left ctrl.

Oh, man! I can't stand inverted axis. xD

Unless it's a flying game or space sim, I'm with you on this. Inverted Y has it's place, despite it making a little more sense in some ways.

I used to use ESDF, it actually works better as it gives you a few more keys on the left to map to additional options. (QWAZ)
But i get few up of having to remap the controls in every game, so now i stick with WASD.
I find it physically impossible to play a game without an inverted mouse. Can't remember the last game i tried it with, but i had to give up after 20 minutes).
though these days most FPSs seem to have the inverted mouse as the default.

It just seems much more natural to me. If I look up in reality, I tilt my head backwards, not forwards. It feels completely wrong to have to move the mouse forwards in order to look upwards.

Strangely enough, I use the same settings when I'm playing an FPS with a controller, but not with a mouse, The controller feels more natural in a way... I somehow want to pull up, on the PC it's more like playing Moorhuhn, no matter how complex the game is: I try to move the mouse towards the spot that I'm trying to hit...

WASD all the way. I keep hearing a lot of good things about ESDF as well but never got around to actually trying.
Heh, just couldn't resist. :P

I prefer WASD. It's better placed, and considering that I have a G15 it makes it easier to reach the macro keys. I used some other peculiar configuration years ago, where all movement except for strafing was done with the mouse, but I've moved away from it almost entirely since I started using WASD.

Interesting. How did you make it work? Left mouse button for forward, right for back? What about alternative fire that some games have?

I'm talking a LONG time ago. When weapons didn't have alt-fire.
EDIT:
Actually there was a few, and then I used ENTER for alt, and CTRL for firing.

WSAD forever :-D

I use the System Shock 2 defaults: WZXC.
I too only invert y-axis in flight and space sims. Which means the cyberspace controls in System Shock totally weird me out. The first couple times in cyberspace, I always end up wobbling around like a drunk because the pitch controls are opposite of what I expect.

WASD all the way since like 10 years or so.
R for reload, Q and E to look around corners, LMB to shoot, RMB for alt fire or aim, spacebar for jumping, ctrl for crouching, X for going prone, F for flashlight and the mousewheel for switching weapons. Also I've bound some keyboard keys to my mouse so I can use stuff like all the vision modes for Splinter Cell without problems or go through an inventory and use the middle mouse button for using/activating.
And I cannot play anything 3D without mouse invert, I got used to it since the beginning and haven't switched ever since. But this setup seems kinda oldschool nowadays in some way, almost all the people I know who got into gaming after me prefer a non-inverted setup.