While windowed mode isn't in the in-game settings, you CAN play the game in windowed mode. Go to C:\Users\user name here\Saved Games\Nightdive Studios\DOOM 64 and open kexengine.cfg. In here, you'll need to change seta v_windowed "0" to seta v_windowed "1" and bingo, windowed mode.

That option is absolutely available in the in-game settings.

Weird, I didn't see that when I looked through the settings... Thanks for the heads-up anyway, that's a lot easier. :)