I just enabled "Run Game in Background" in X3: Terran Conflict. But I don't know how it works - do I just minimize or what?
Normally, X3:TC pauses when the game is not 'in focus'. If you wish the game to continue processing while you are alt-tabbed out, then enable that mode. This is beneficial in some ways such as allowing your factories and complexes to continue to operate and produce profits, but you also risk the possibility of your ship being blown up by invading Xenon or even pirates when you are not paying attention.
Also, there are built in flags that cause random pirates to spawn to attack your complexes, auto traders, etc when you remain idle in SETA mode for long periods of time.