For a good Anti-Missile Defense, if your focusing on beams, Gauss Cannons rule supreme.
If you have a little Missile research, build AMMs (Size 1, 1 point Warhead) with R1 Firecontrols, and have dedicated AMM ships.
If you want to focus on just one weapon, Lasers are the way to go, small calibers have High DPS and good fire rate, High calibers have awesome armor penetration.
If you want to quickly exaust enemy missile supplies, get one of your standard freighter designs, slap 2 CiWS and 20 levels of armor on it, activate the transponder, and charge the enemy fleet.