It's been awhile since I played, but I haven't seen these mentioned here.
Troopship bays are typically *much* more efficient than the equivalent amount of colonizer bays. A ship with one colonizer and 1-3 troopship modules a quite efficient colonizer that doubles as a troop transport when needed. Particularly useful ferrying colonist to a new colony that you *did* just use a single colonizer on.
It's rather 'munchkiny' but if you seem to have a lot of anomalies in a game, stick survey modules on the smallest ships you can, wind up the tiny little keys and toss them out (I've also been known to put them on Asteroid Miners) and grab anomalies en-passant - they're slow, but as your territory expands you have them everywhere and no one else ever builds them. Particularly useful in combination with the speed boost Civ bonus.
Theory: (Untested) Due to the odd way the system breaks ties, a ship down to one hitpoint and a lot of weapons can survive encounter after encounter if it outguns other ships. A, ah, Cargo ship has only 1 hitpoint.