Silent Hill has some awkward controls.

The problem with console controls is that they're shit for accuracy and they require you to bring a controller with you when you travel. Keyboard + mouse really ought to be good enough for most games. Some games like flight sims you really want to have a joystick, but games shouldn't be unplayable without a controller.

FO3 wasn't that bad, but it definitely did play a lot better once I got a controller. In that case you were already paying the price for it being a console port in terms of accuracy, so you might as well just use a controller.

Yeah you don't really understand just how strong the auto-aim is in FO3 until you use a laser weapon with mouse aiming. I ended up modding the auto-aim down to almost zero because it actually made it HARDER for me to hit what I was aiming for. In terms of actual control schemes though it was fine. It was particularly better than Skyrim, which doesn't really have a bad control scheme, but it does have the worst UI known to man.

Right now I can remember these:

Alone in the Dark (latest game from the series) - Terrible moving controls, PS 3 version was enhanced, but PC versions didn't get any patch :(
Resident Evil 4 - Don't even think about playing this game on the PC without a gamepad.
In Cold Blood
... there are many other games with not very good controls which I can't remember right now. But even with their flaws I like these games, if they have other qualities.

That's just the problem, the only way it can be addressed is via autoaim and or screwing with tolerance. There just isn't the capacity for precision with a nub that you can get with a mouse. Especially somebody that's gotten used to using a mouse can very quickly hit a tiny portion of the screen.

The way that they make controllers work these days is by removing the accuracy requirement via auto-aim or increased tolerance both of which are just workarounds for the fact that controllers lack the necessary delicacy to handle those sorts of games.
It's a trade off with some genres of game. With any FPS it effectively can't be done as you'd have to rebalance the game for controllers and keyboard+mouse. Other genres are more forgiving and could handle both without too much trouble.

I'd love to see those Halo players go up against the Quake and Unreal players mixing it up between console and computers, but I have a hard time believing that it will ever be possible. Consoles generally cheat to make it work. I lost the link, but there's a great blurb from one of the developers of Halo about how much cheating they had to do to make online play work.

Also, consoles have always had controllers going back to the days of pong, they're not going to add a keyboard and mouse because that would be more expensive and people who want that tend to buy PC games anyways. They ended up with the standard gamepad because it was flexible and was generally the least bad option they had available.

I'm not sure what you mean, tbh I only use gamepads for racegames.
Assuming you refer to PC gaming, almost every PC game I know of can be configured to use any form of controller natively and if not manufacturer software or 3rd party software (JoyToKey or Xpadder) can be used.
You can even use software so you can use headmovements to emulate the mouse (blink your eye to shoot xD).
Can't say the same for a console, try to hook on a mouse or keyboard and make it work with a game and a gamepad generally means a lack of buttons of which most are controlled by the same four fingers while six fingers aren't used at all and that also limits the options in a game which have to be adressed by awkward interface designs.

No problems with Tomb Raider here, both old and new series.

I do have problems with Bloodrayne (either 1 or 2, can't remember) controls though. Non-existent save game anytime anywhere system certainly does not help either.

Can't believe that no-one has mentioned Prince Of Persia: Sands of time. They made the controls camera relative, then introduced a camera that randomly switched to new perspectives mid move. You'd be carefully running along a wall to avoid a spinning blade thing, and the camera would switch, and you'd suddenly veer straight into the blades!

I honestly don't understand peoples dislike of the tank-like controls of resident evi and silent hill honestly they are not that hard to control

I survived the Ultima Underworld and System Shock controls, so any controls feel "fine" to me after them.

That said:

I never really figured out that well how you are supposed to hit the slow-moving zombies. If I tried to hit their head (the only way to kill them without using all your bullets?), 90% of the time I'd miss with my shots.

Yeah, I have a copy of that game and gave up fairly quickly as it would change at the worst times. I'd have issues in AC with that when I was hitting up the assassins' tombs, but it was workable and I got my gear.

That was partially a camera problem in PoP and partially a controls problem as they would effectively remap the controls as you worked them. AC at least had more predictability so you could see it coming during the tomb sequences.

Anybody remembering the first RTS games. Those before "right clicking". Today I consider Warcraft and Dune II pretty much unplayable. No "drag box" and hitting "attack" and "move" everytime to issue the order really isn't doable for me anymore.

GOTHIC. For fuck's sake, GOTHIC.

This might be PC gamer blasphemy but I also hate when games make me use the function keys. I'm just terrible at finding them quickly.

The handgun is a piss-poor weapon that you use to whittle away a zombie's health from as long a distance as you can without the camera screwing up your aim; if you're lucky, you might down two of the bastards with one clip. I know it doesn't make much sense that you can't aim properly no matter the range, but it encourages you to run away and conserve ammunition. As far as I remember, the shotgun (and possibly the magnum) is the only headshot weapon, and even then you have to aim at the sky and wait for a zombie to be practically on top of you.