If you know how to use command line, you can run
tremulous.exe +set r_height 400 +set r_width 640
If you don't know what command line is, then you can just delete your autogen.cfg in
%APPDATA%\Tremulous\base
or
%APPDATA%\Tremulous\gpp
if you are running GPP.
If you don't want to lose all the settings stored in those files, you can just edit those files and change the values of r_height and r_width.