Cheat Mode
Press [Enter] while playing, then type:

Code - Result:

kobayashimaru - Skip to Next Mission
showmethemoney - Increases Money
phonehome - Chat List in Multiplayer Mode
screwyouguysimgoinghome - Boot List in Multiplayer Mode
canofwhoopass - Activate Limited AI Over Your Ships
imouttastepwithreality - Enter Gamma Quadrant
youstopmecold - Faster Ship Production
avoidance - Faster Crew Production

Invulerability
First open the file RTS_CFG.H. Go to the line under difficulty settings and modify the line which says:

float EASY_DAMAGE = 0.5;
or
float HARD_DAMAGE = 2.0;
to
float EASY_DAMAGE = 0.0;
or
float HARD_DAMAGE = 0.0; or whatever you want.

Higher numbers make it harder. Then set the game difficulty to Easy or Hard. This will make your shields impervious to normal weapons fire. Any specials that naturally kill shields will still work.

Transport More People
Modify the same file as above (RTS_CFG.H.) and look for the line TRANSPORTER_MAX = 5;. Change this number to something higher and your transporters will carry more people each time.

Unlimited Money Trick
This cheat will allow any player with access to a NEBULA class starship with the GEMINI EFFECT to a source of unlimited money. To do this have your NEBULA class parked close to a ship yard with another ship (should be a ship which can be quickly dismantled, (any of the first three classes of ships should work fine)) parked close. Fire the GEMINI EFFECT onto this ship and once it hits have the cloned ship sent for dismantling. If done quickly enough you will gain money for the dismantled ship, without losing any ships this process can then be repeated as many times as needed as a continuous source of money.

Super weapon:
When playing as the Federation, seize control over a Klingon shockwave ship or the Romulan ship that creates the rip in space. After getting it, build a Nebulae class and research Gemini Effect. Use Gemini Effect on the captured super weapon and you then get two. You can identify them by seeing which super weapon has least amount of energy. Move quickly and use the copy of the super weapon. You can do massive damage to anyone, though the copy only lasts fifteen to thirty seconds. Use it as many times as desired.