I use windowed almost exclusively. In nwn.ini I jammed:
Those settings are there initially, just replace values. If the game chokes on them, I think it resets to 800x600. Game needs to be off to edit that ini, it only reads on load and overwrites on exit.
In game, since I have a 16:9 monitor it gives me barely any resolution settings, but I think there were lots of options for 16:10 monitors. Anyway, the game window isn't quite those dimensions, but it's pretty close, everything looks good (no scaling artifacts...but I think there's only a few real visual modes and changes just crop the non-gui graphics displayed).
Can't find a handy list of supported resolutions to link to easily.