What do ship commands do?

Sentry and guard are variations on a theme. Sentry will put a ship on hold until another ship belonging to another race flies within sensor range. Guard will do the same, but will only respond to hostiles.

Autosurvey will send any ship with a survey module off to hunt down anomalies.

Autoexplore will send a ship to the nearest unknown area, and will generally explore the entire map in the most inefficient manner possible until its entirely revealed.

Construct will light up for constructors, which will trigger the construction of an economic, military or influence starbase in their current location.

Destroy will scuttle the ship for a small cash bonus.

Be warned on sentry, it will respond to freigters running trade routes, even in their reduced background mode. Position accordingly, if you don't want to continually have to reset the sentry mode.

I see, thanks. I generally play smaller maps, so I don't have much of a use for this. How does auto-attack work? It's fairly self-explanatory, but how does a ship decide whether or not to attack? Is it based on range or engines?

How does auto-attack work?

The ship just makes a bee-line for the nearest hostile and gets down to business, IIRC.

What about Auto-Retreat?

It runs away from danger as fast as it can. Basically you've told it to do everything it can to avoida fight.

Auto-attack behaves rather erratically.

Sometimes the ships will fail to see enemies three squares away, sometimes it will attack any ship belonging to a race less than Neutral in relations to you, whether you're at war or not.

And only in the Star Trek Mod have I see the Auto-attack AI actually attack ships in orbit around a planet (I actually shed tears of joy)