The fs_game_base cvar let's you set an additional search path between base/ and your fs_game directory. This lets you base a mod off more assets than just base/.
In Doom3 for instance this will let you mod the Resurection of Evil expansion pak and use content from both Doom3 and ROE.
In Quake4 since no official expansion pak has been announced, this feature can be used between various mod fs_game directories.