The weapons I typically use for my primary batteries are Missile-Beam-Punch, Cannon-Cannon-Punch, Beam-Cannon-Punch, and Beam-Beam-Ion. Which three I use is dependant on what roll I envisioned for the ship, but I've found dividing the volume of blocks you have by roughly 1/3 and allocating 1/3 to a missile battery, 1/3 to an ion beam, and 1/3 to a continuous fire cannon or beam seems to result in a nice balanced ship.
If I want to make a more missile heavy ship, I'll make my ion beam, or cannon system smaller and put the extra blocks into a 2nd missile battery. I've also made a specialized variant of a destroyer with no missile, but a 15,000 block beam system. That one worked pretty well versus missile heavy ships, but would get ripped to shreds against a cannon heavy ship. I've also noticed that a cannon heavy ship will lose to a missile ship with forward firing full beam missiles. However, vertical launch missiles tend to have a better chance of getting through AMS fire at a moderate range but are horrible at point blank, they'll spend several seconds looping around the target taking AMS fire before impacting. So the above mentioned cannon heavy brawler would do extremely well versus the exact same ship it would lose to, if that ship simply had a VLM battery.
Really, the weapons you choose are dependant how fast your ship is, at what range you plan on engaging your targets, how solid is your AMS system, and what you think those targets will have to shoot back at you. That's one of the cool things about Starmade, there is no weapon mix that is blatantly superior versus every other ship in every other situation. You could even make a few different variants of your ship with different super weapons set up to engage different targets.