This isn't "I always change the controls to my favored settings", this is more you were playing a game whose default scheme was fine for it, but then you started changing things because you got used to it.

I recall putting the aim key on shift in New Vegas because I was fresh off playing FEAR. It doesn't have sprint so I was fine doing that, and I don't really like having the use key on E unless the middle mouse button is useful for something else, like how I switched the zoom in Saints Row 2 to MMB because I was playing Warhammer 40k: Space Marine right before that.

I was tempted to make the quick save key in Doom 3 BFG to F6 because I was playing STALKER before that, but then F5 wasn't really worth changing it to F6.

Weird how priming works.

I rarely do much key rebinding. A notable exception is Broforce, whose developers seem to have been actively hostile to the idea that anyone might play their game with a keyboard (despite the fact that its gameplay doesn't benefit from analogue sticks at all), and so don't seem to have given much thought to what a decent layout would be. After several sessions of experimentation, I wound up loosely basing my custom setup on Spelunky Classic's controls.

Yes all the time. If you own a mouse with extra buttons like the Logitech G300S, you can bind them to mimic pressing mostly unused keyboard keys, eg punctuation keys like ;'#@ or the Numpad /*-+. keys, then in each game rebind the same keys, then you soon get used to having certain extra mouse buttons activate a specific commonly used command. Eg, top-right = Inventory, bottom-right = Map, bottom-left = Flashlight, top-left = Crafting, etc, and gameplay is then so smooth & fluid in many games when you can access these commonly used commands via the mouse without needing to take your "keyboard hand" off the WASD / cursor movement keys.

Quick Save/Load to F5/F9 because I do these actions mechanically and accidentally mistaking one of those could be pretty bad :D

I don't also like "WASD" games using TAB because I often hit Caps Lock instead, so if it's something important I would change it.

Crouch/sneak from C to left Alt because holding it feels more natural and comfortable to me.

Same, but I use Left Ctrl cause it's more comfortable for pressing it by little finger.

I, on the other hand, always immeditely rebind crouch to C whenever a game does not have it that way by default (usually from left CTRL). Which is most games these days.

So many genres I can't play unless I can rebind the keys, and that's a lot of rebinding.

I actually mouse left-handed. And WASD was *never* good. I use numberpad, so I always bind around there. Some giems don't detect numberpad keys correctly (ignoring numenter is common). But I usually do something like:
8426 for movement, 5 for jumping, 0 for crouching, + for quick heal, /*- for menus (like level up or inventory or open map), enter for interact,, etc.

Interesting. Do you really prefer 2 instead of 5 for backwards movement? When I play splitscreen with someone, I usually use the num keys, but I use 5 for moving back, so that the layout simulates WASD or arrow keys.

Yeah, I never liked crouch on Ctrl, so I bind it to C. Maybe my hands are too large for this keyboard, but with WASD, my pinky rests naturally on the shift key, and contorting it forces the rest of the hand to inch a bit, whereas with C, my index used for about everything else, so crouching is just another function for it. I also make crouch modal when given the option.

I do. That gives me access to 5 for jumping. Mind you, I've done this since the 90s, so my paws are used to it.

I guess you are talking about when a game won't let you rebind, and so you have to tolerate as is, and after time you get used to it.

For me, that isn't how it works. I don't really work on that principle. I rebind keys to be logical the way my hand sits and for comfort, ease of use and speed.

Most games let you rebind, so I am no going to let some stupid game that doesn't, dictate to me beyond itself.

Just for the record, I am right-handed, and so I steer my mouse with that, and use the right mouse button to move forward, the left mouse button to fire. With my left hand, I use the space bar to jump and right CTRL to crouch, less than for slide left, more than for slide right, and question mark for reverse. That's my basic bindings. With the rest I try to stick to first letter bindings, such as C for crosshair, F for flashlight, M for mouselook, I for inventory and so on.

If I'm playing F1 games or racing sims on keyboard rather than my wheel, I'll usually go for AZ,. (classic Geoff Crammond's Grand Prix scheme) or Space CTRL Left Right (Codemasters F1)

The only time I've ever had to rebind keys that I remember is in the Jedi Knight games where I assigned all the forces powers very specifically to keys around my pinky.

Got super accustom to changing every game to use the TAB key as my inventory. Saves time remapping my keyboard than my brain ^_^