I found it quite amusing to simply take out their life support until they all die of oxygen deprevation (yes, I know that makes me an evil bastard), but, on the bright side you get a lot of scrap

If they have 2 shields and you have the standard 3 damage laser, its quite easy to keep taking out their O2 supply, with the odd fire to take out their health too. if they have plenty of spare hit points on their ship, taking out their med-bay if they have one is great too.
On some of the smaller ships, they don't have access to their O2 room, so one volley to take out their O2 supply, then sit and wait until yo uget all your shiny scrap
