Here's some stuff I've used as standard on ships ranging all levels (not all at the same time obviously!):
- Bombs are pretty much the go-to weapon for all your needs
- Lightning fields
- EMP Wave
- Pulsar generators (does not affect planets)
- Missiles (always have a faster or mass killing weapon as backup)
It all depends how you build your toy
All of those are viable. My current setup since level 40 or so, and up to my current 85 is: bomb, laser, lightning field, virus weapon. With one energy leech for regen, I can keep it up indefinitely.
Weakness of fighters is that once they start going down in a mob, you're screwed unless you have a massive energy store.