Call of Duty 5: Starting Mods
Since Patch 1.1 release 11/11/2008 the fs_game is set to default to fs_localAppData.
This means that to run your Mods you need to place the .CFG and .IWD fies here on the server:
"C:\Documents and Settings\Username\Local Settings\Application Data\Activision\CoDWaW"
Of course replace Username by your Username on the server.