I haven't played a first person shooter (or any computer game) in years (ever since my computer become obsolete for gaming). But back in the day, I used to try and use the same configuration for every game:
Up Arrow Key - Move forward
Down Arrow Key - Move backwards
Left & Right Arrows - Strafe left and right
Enter - Use/Activate door
Shift - Jump
Ins/0 Number Key - Toggle Walk/Run
Right Control Key - Crouch (hold)
Delete - Reload
Mouse Wheel - Change Weapons
Mouse Button 1 - Fire
Mouse Button 2 - Alternate Fire
End, Page Up/Down, Home, the Number Pad keys, and the Mouse 3 button were used to operate the various options that were game specific (in AvP, they controled vision types, flares, etc. In Deus Ex, End shut off all augmentations, and the Number Pad keys toggled the heads up displays on and off. In Ranbow 6, the Page Up and Down keys switched through my teams. etc).
Personally, I find that having less keys directly touching the arrow keys makes it easier to find what you're looking for without looking at the keyboard (which is perfect for playing in darkness), and it keeps me from hitting the wrong thing at the wrong time and potentially blowing myself up.