Use Ionic Dispersers
I sent this in as a (possible) bug a few days ago. I mean, engine destroying weapons destroying a satelite with *no engines*. Heh
Other than that, I just use EAGs (can't do without Organics).
This also works well against fighters (2-3 destroyed each shot), and is really useful when you have a bunch of boarding (or crew conVersion) ships and a few repair ships in a fleet.