So I need to uninstall STO.
I loved it but I'm involved with another MMO and my group needs a new leader and it turns out I'm it.
So I had a worm that killed most of the .exe files on my computer including the "Uninstall Star Trek Online.exe" file.
So... Now I can't uninstall STO.
delete the folder, though if you're really worried about shortcuts or registry entries, you can manually delete those or use a registry cleaner. Or you can just reinstall to the same location and uninstall like the other guy said.
If you are running Vista/Win7 you will want to run the uninstaller or the game won't be unregistered from the Games Explorer. Granted if that doesn't bother you then just delete the files and the Star Trek Online registry key.