Huh, seems weird to not use your pointer finger for D/strafe right, and for F with is usually a secondary action of some sort (I have the 'use' key bound to the fourth mouse button usually). I've actually bound crouch to shift in a few games because it is slightly easier to reach than control and sprint is spacebar. In a game that actually supports crouch-jumping I'll have shift as jump and ctrl as crouch, that way a crouch jump is me rolling my pinky down the keys, as if pushing one button with my whole finger tip-first. Much of it depends on how much jumping is required in the game. In ARMA games sprint is W + S so holding W I can roll my finger back on the S key similar to what I described above to go into a sprint.
Having the option for toggling and pressing various keys would also be nice. For example, in many games I'm not a fan of toggling 'aim down sights' mode as it's faster for me to let go of the button when I'm done than to click it again (and speed is important in FPS games before you say anything). In games like Red orchestra I actually have toggle and hold keys bound for crouch, for when I need it for a second or so, and for when I think I'll be staying in a spot for a minute.
(Comments posted as I was posting. Hadn't thought of left-handed. There where EDSF binding in Tribes 2 which would obviously allow a few more keys to be accessed on the left side of your fingers, but it felt slightly too cramped for me for some reason so I just use WSAD. I do wish that caps lock were swapped with the | key though because it is a bit annoying enabling caps lock if you want to use that button, and if you don't then it's just a button that could be used but isn't.)
Once upon a time (OFP) I used arrow keys for stuff. Yeah...
Okay, I suppose that brings up... not quite a pet peeve, but a sort of wish.
Dear game devs: allows us to have whatever crazy key combinations we want, and as many of them as we want for our controls.
Now for an actual pet peeve: lack of cheat codes
It seems cheat codes have pretty much died out as far as I can tell. They shouldn't be things given to you, you should have to find them yourself whether by an easter egg or searching the internet. Maybe you're told what they are after you beat the game on a certain difficulty setting, but you shouldn't be locked out of you if you know the code because then it's not a cheat code it's an unlockable of some sort.
I don't agree with having cheats in multiplayer games, unless there's some exceptional circumstance and it's some kind of sandbox/fun mode where people dick around. Cheat codes could also disable things like achievements and certain progression systems that would rely on playing fairly. They're just something for you to do for fun. I remember after beating Half-Life 2 I would go around the levels setting up scenarios where AI would fight each other, and that wouldn't have been possible without cheats or console commands. There's also all sorts of fun things you can do with cheat codes, and it's a way for people to squeeze more enjoyment out of a game the way they choose.