When the "Balance Of Terror" mission starts, type "knat attack", before going to warp. Then, the Starbase will disappear and Knats with the names of the development team will appear.
Reload Photon Torpedoes
After the first battle of mission 7, type "****tiberius", then enter within transporter range of the Starbase, and press I.
Fire While Cloaked
Select the "Create Mission" option and choose any ship with a cloak. Then while playing a game, type "car".
Powered-up Photon Torpedoes
In the "Omega 12-300" mission, type "$punish".
In the "Smugglers Den" mission, type "$->me!".
Kill the Romulan near Raven
In the "End Game" mission, type "mercury".