For secondaries, I too nominate the Treb, but not just for its bomber-downing capabilities. In missions such as "Their Finest Hour", I like to use the treb to knock out beam weapons on cruisers from outside their range.
A close second is the Tornado, which is better than the treb for taking out fighters. A single volley is almost guarenteed to destroy any shivan fighter, and even a Nahema at close range.
For primaries, the Kayser is the obvious choice, with the Maxim a close second.
However, all of these are nothing unless they are mounted properly on the correct fighter. While many people choose the Erinyes with its 8 primaries and better maneuverability, but I prefer the Ares. Its slow, but it's heavily armored. For most missions, I chose this mounted with 4 kaysers and 2 maxim, especialy when going against bombers, its the reverse if there are more cap-ships to engage, then secondary bank 1 with Tornadoes and 2 of trebs, but if the threat is almost exclusively bombers, then I grab as many trebs as I can mount.
Later!