Close the game, go to config/client/prefs.cs, open it with notepad.
Ctrl+F for $pref::Video::resolution
Format is:
$pref::Video::resolution = "width height bit-depth refresh-rate";
Use 32 for a bit-depth, if your computer can't handle that for some reason, you shouldn't be playing bigger than 800x600 windowed anyways.
And just for safe measure, go down a few lines to $pref::Video::windowedRes and change it to match, but only width and height.