Blaze72: Always having to have to name your save slot.
The very same problem existed in the original DOS version (try OUWB with DOSBox, and yeah it's annoying).
In E1M2, in the bookshop near the phone booths in Miskatonic Station, the cash register only acts as a switch once, I'm pretty sure it was reusable in OUWB.
Random bugs/glitches/annoyances I've found :
Floating blood splatters
Less gore when enemies explode
Sometimes Cultists speak like Fanatics (and vice-versa -pitch error)
AI borked (too much infighting, and Cultists sometimes on the easier difficulties do the "dynamite throwing" gesture while lauching nothing, "disable run glitch" on or off.
Also enemies behave much more erratically, sometimes Zombies when getting back up on their feet will ignore you for a short while, in the original (even nBlood and BloodGDX) they are relentless.
Too much Cultist and Fanatic accuracy (pinpoint even on Still Kicking)
Other switches working only once (can't remember the maps right now).
Save system borked, why use F2/F3 for QS and require the menu for manual save? Why not have two sets of save keys?
Also quicksaving takes far too long and pressing F3 with no quicksave softlocks the game on the "Loading Game <EMPTY>" screen, freezing it in the process (and no way of re-focusing Windows on another program/desktop windows). I was thinking it's open the "Load game" menu and I wanted to check if there were autosaves like in BloodGDX.
Changing the video driver or turning VSync on/off the clicking "APPLY" either crashes and freezes the game, or just freezes it.
When I turn Vsync off, I have to "alt-tab" (by ctrl+alt+del, then choosing Task Manager to refocus Windows) then alt-tab back to the game.
Also Caleb has too much running velocity and too much jumping height, while it helps it sometimes breaks the level sequence since he can make high jumps out of the water. However Caleb doesn't have Duke's athleticism and should jump as high, IIRC.
Clunky key binding menu, when you reassign an already assigned key, no warning, you have to go to the option and "re-bind" the key to remove it from the menu item.
Those are the ones I remember.