It does really depend on what you're up against. I would recommend building more fighters than bombers as they are better against more types of ships. Transitive had it pegged
its basically impossible to use bombers at all unless you've already got total air superiority in the grav well, which is the real reason we like fighters so much. you add the bombers in only once you're sure they won't just get killed on the way in.
So here's some tips on using bombers effectively:
1) Keep bombers docked until you're ready to use them.
2) If there are fighters in the well:
a.) Use bombers on a launch and recall basis, launch against a few targets and then recall and dock them.
b.) Remember that to fighters, bombers are priority 1, so unless they have pre-ordained targets, they'll target your bombers next, the longer they're out, the less you will have.
c.) Draw fighters away from your carriers with your own fighters by using the local area attack range and moving them to the opposite side of the gravwell before launching your bombers.
d.) Move your bomber carriers as close to your target(s) as possible without entering firing range before launching.
3) Bombers are great in hunting down fleeing cap ships, if you see one trying to get away launch your bombers after it, most of the time, it'll be toast.
4) Anti-matter is everything to carriers, without it they are useless. Adding AM enhancing ships, structures and techs will help you out a lot.
With enough micro management you can kick some ass with bombers, but NEVER rely solely on them. Fighters are generally the way to go.