Saints Row 2.
While it was actually a pretty good game, it's legendary for how bad the controls were.
It was ported from console (one of the earlier ports) and whoever decided the controls had clearly never played PC before and no one bothered to test it, they just slapped whatever sounded good on paper.
Aiming was the biggest gripe.
You couldn't just right click, aiming was done with V. Scopes were brought up with V but then zoomed with H to zoom in and N to zoom out, which you were always doing. This meant one of your hands was being removed from primary controls when doing so. When finished you had to hit V again to shop aiming. The same happened with member interactions where recruiting was done with up/down arrows and taunts and compliments were left/right.
It was a mess.
Saints Row 2's controls were perfectly fine on console though, at least on Xbox 360 where I first played it. (I couldn't afford PC gaming then)
Most shoddy PC ports control horribly, like Dark Souls, and the Attack on Titan games. Someone I know always quips that Japanese developers only care about console.
The only problem I've had with Rockstar games on PC vs console is the weapon wheel. The whole mechanic is designed around analogue sticks. I don't mind the realistic animations at all, realism is one of the major appeals of their games.
Mad Cat's controllers in the 90's and 00's were horrific. I couldn't stand them, and yet somehow, I always wound up with one, because even though it was terrible, it was an extra controller for when a friend was over.
The roughest controls go to Dwarf Fortress, I love that game to pieces, but teaching it to someone is an exercise in patience, and this is assuming they understand computers fine, and are REALLY interested in learning.
Yeah, Mad Catz made some of the worst controllers around, along with Pelican. It is a miracle that company survived as long as it did. I'm surprised they even bothered coming back now under the same name.
I'm not comprehending all of the hate for Xbox controllers here. It seems to me that the lineage of the modern controller stems from the Dreamcast, and continues through the iterations of Xbox controllers. It was the first, to my knowledge, somewhat ergonomic general-purpose controller. The analogue, spring-equipped triggers were the real clincher, but the analogue stick being above the d-pad made more sense in 3D titles as well. The Playstation's dual analogue sticks were certainly important, and the controller was infinitely better than the N64 controller even if it had only had one of them, but the layout always seems to me to be more oriented towards traditional JRPGs, or something, vs anything that wasn't turn-based or heavy on menus. The 4 bumpers were also, of course, ahead of their time. The original Xbox, even with The Duke seemed to finally get the the layout almost just right. I didn't seem to really mind The Duke at all other than the placement of the white and black buttons, and the s type was far and away the best controller of that generation. Perfect for FPS and driving alike. 360 and XB1 seem to have just refined the ergonomics, which is certainly still an improvement. The PS4 controller, by comparison, seems like a step back from the PS3 controller, which itself seemed like a remnant of the mid 1990s.
I'll preface this with the fact that I loved the Nintendo 64 in its entirety. Some of the best games, especially shooters, ever made were released on that console.
I consider the N64 controller to be the worst controller I have ever used, possibly tied with the GC controller. Physically limiting the directions of movement on the analogue stick (and later c stick) with abrupt corners was beyond infuriating, the 64's layout was confused, nonsensical. The GC's giant marshmallow buttons were awkward and even often got stuck, even on the official Nintendo controllers. The layout, while improved, was easily the worst of that generation. The Wii's bizarre nunchuk and wand setup wasn't much better, I may have even preferred a crappy old GC controller if I had bothered to play that console enough to care. I find it ironically indicative of Nintendo's reputation for gimmicks to have the gall to call the most usable controller they had ever produced to that date the "classic" controller. I haven't used the Wii U at all, or the Switch, but those new bluetooth controllers that they slapped on a 1st gen Nvidia Shield don't look too usable to me either.
I, unlike some others, quite liked the NES controller. I would agree that the 2600 joystick wasn't great. We have some sort of red and black knockoff joystick with a white button on top of the joystick that feels much less stiff, and allows greater leverage. I would say the Sega Genesis controller was probably the best of the ones I have tried from the 80s.
On a side note, have you guys ever seen one of these? They have turbo buttons, and a more ergonomic design. I can tell that that slider ... thing is basically useless. I have one, it just flops around. I have never tried to play anything using it yet though, just another one of those Goodwill, "What the hell is that? That's cool." Moments.