Transcendence can be run with a number of command line swiches:
/debug runs the game in debug mode, allow access to the console (F9 ingame)
/dx forces DirectX
/nodx forces GDI
/exclusive
/debugvideo extra graphics debug lines in debug.log, paints framerates ingame
/windowed runs the game in windowed mode
/1024 switch to force into 1024×768
Please note that Transcendence uses (as default) GDI under Windows XP, and DirectX under Vista.