Creating Desktop Shortcuts for TDM
From The DarkMod Wiki
To create a desktop shortcut for The Dark Mod, just create a copy the existing Doom 3 shortcut (or create a new one to the file Doom3.exe). In this example, the Doom 3 installation is in C:\Games\Doom3. Change the command line to this
C:\Games\Doom3\DOOM3.exe +set r_fullscreen 1 +set fs_game darkmod
This should advise the engine to open the Dark Mod by default.