First, you only need 2 kinds of ship for combat: Siege ships and Point Defense ships. A Point defence ship is self-explainatory, although there are certain tweeks you will want to consider. Just because you have a new beam weapon available doesn't mean you need to rush it into production. Often a lower-tech weapon with plenty of upgrades works better. For point defense, I've found the best weapons thus far have been Hard Beams, Ion Cannons, and Phasers. Use them with Improved, Autofire, and two levels of Miniturization whenever possible. Lightning Shields are the best last-ditch PD weapon, and should be included as a back-up on PD ship. However, your primary two banks should be one type of weapon on a PD mount and a secondary weapon on a Light Mount, so that the range is slightly higher. More on this soon.
A Siege Ship is simply a ship devoid of any beam weapons. An even mix of fighters and missiles is the idea. When using fighters, just use Interceptors, as Space Superiority fighter aren't really worth the extra cost. When using missiles, larger warheads may seem nice as first but in acutality hinder this design. Instead, go for the old Robotech technique and load up your best missile into 8 shot racks of Point Defense chassis. Why? Because then you'll be firing off a volley every second, and in large numbers. This will overwhelm almost all enemy PD systems with rapid waves of missiles, enable you to take out fighters, and throw so many missiles into space at once that their guns will never be able to stop them all.
Now here's the kicker: Make both of these ships SLOW. That's right - go in and drop their System Drives down to a speed of 250. Now you can use all that extra space (and you will see a BIG difference, too) to load up with more weaponry.
The idea is simple: All your fighters and ordinance will attack the enemy fleet or planet on their own, while you remain in the back of the scene. Why stick your own neck out?
However, it is on the defensive where this idea really pays off. Since all ships are moving at a snails pace, your entire fleet won't be able to break up during the fight. Even with ten armadas, you'll just two rows of five armads each (or a defensive ring around your planet, if you're defending). Remember the Light Mount defense guns? Weapons with a range of 8K to 12K will be overlapping other formations. This, if an enemy fighter wave targets one of your formations, they will take PD fire from as many as four or five of your defending ships.