Federation Commander

I have seen a lot of talk of hit and run on the form and in the rulebook, but exactly is it?

In it's simplest form, it's a targeted attack by a marine combat squad.
See rule (5F1) RAIDS ON ENEMY SHIPS

[Mod: Deleted rules text, as it is unnecessary. Just read the rule from the rulebook.

P.S. This is not a warning or anything. Just deleting the unnecessary text.]

You use your marine baording parties to "attack" a specific box on the enemies ship. If he has two torpedo mounts remaining, one charged and one discharged... an internal hit scored on "TORP" will be scored against the discharged weapon. With a Hit and Run raid, you can specifically target the armed weapon (and possibly destory it before he can fire it).

Or, if you're last drone is being held in a tractor beam, a Hit and Run raid against the offending tractor box may cause the drone to impact!
Want to take out the Plasma-R on a King Eagle? Use a H&R raid. Need to disable a web generator on a Tholian cruiser? Use an H&R raid... and so on.

And if you want to really nobble that King eagle then H&R his cloaking device - H&R is the only way of taking a cloak device out.