Cheat Codes:
Here's a simple cheat to give the Enterprise almost one thousand torpedoes! (makes it easier to win all space battles):
You should make a backup of your save-game files before doing this - just incase you make a mistake.
Using a hex file editor (download one at: http://www.shareware.com/ - just search for "hex editor" and you'll find heaps) edit a saved-game file - located in the "SaveGame" directory where you installed the game. Their names are like: "GenSave.da0", etc.
Bytes $128 and $129 (these are hex-locations) store the quantity of photon-torpedoes remaining. You start with 275. Thus, if you still have 275 torpedoes, then these bytes will be: $13 and $01 respectively. (the bytes are in reverse order - actual hex value is $0113). These bytes will just be something less if you've already used some torpedoes.
Simply edit byte $128 to: $E0. Then edit byte $129 to: $03. You must only replace these bytes - not insert bytes! The file size must remain the same. Then save the file.
Next time you load the game (from a save-game file that you edited) and go into a space-battle, you'll notice that you have well over 900 torpedoes!
No more worries about running out of torpedoes now. This is especially useful in the last battle against the 11 ships (3 Romulans, 3 Chodak, and 5 Klingons).
I've found the easiest way to beat enemy ships, is to target their weapons-systems first, then when they're knocked out, destroy their energy sources, then whatever after that to destroy the whole ship. Once their weapons are gone, you can just use the phasers to destroy the other systems if you want to save torpedoes - not that that matters anymore though now with this cheat! The klingon "birds of prey" can be easily destroyed using only phasers, but it is quicker to just torpedoe them too.
To speed up the rate of reloading of torpedoes, set the life-support energy to maximum.
When the enemy fleet is together, the best strategy is to stay just within your torpedoe-range (<40,000), and keep launching torpedoes at them. This can be done by using the "Maintain distance to target" command initially, then using the "+" and "-" keys to get the distance exact for better control. Once you've damaged the first ship enough, target the next closest ship immediately afterwards. This takes a bit of practice, but I've managed to easily destroy all 3 Chodak ships like this (best to wait until all ship systems are fully repaired before going into the next phase of this battle - i.e. after destroying the 3 Romulans). I've finished the whole game (only finding and using this torpedoe cheat in this last battle), like this. I've always been using the easiest (Ensign) level though. The game is difficult enough to complete even on this level.
However, I noticed that there are many other plot flows, and other missions that can be done if you aren't 100% successful in each mission prior to this.