FF7 on the PC. With some fan-made patches, it actually runs 100% fine. But... oh god the controls. They can't be changed. Everything is mapped to the num pad. So 8426 are the arrows and the other ten buttons on the PSX are random other things. And to top it all off, everything is still referred to ingame as circle, square, L1, R2, etc.
Also, Goldeneye. You can't customize the controls, though it does have a few different control schemes. Most of them, the analog stick up/down makes you move, but the stick left/right makes you look. The yellow buttons are the the other way around: up/down is look, left/right is move. Then there's the last one, which almost emulates dual analogs... except the stick (left thumb) is look and the buttons (right thumb) are move, the opposite of every modern shooter. I got pretty good at the game as a kid, but nowadays I find it unplayable. (It is the game that made me an inverted player for life, though, so shoutout to that.)