A recent run with the Zoltan A netted me two Halberd beams, a Burst II, and a Pre-igniter (plus cloaking).
Pretty much every battle after sector 4 went as follows:
Burst-L 2 drops shields
Halberds carve ship into tiny bits.
Not dead? Cloak III and wait for all weapons to charge, while enemy crew pisses themselves in fear.
Cloak ends: repeat Step 1-2. Watch the pretty pretty explosions.
...The flagship lasted marginally longer, due to switching out one of the Halberds for a second pew-pew gun. By that time, a single Burst 2 wasn't cutting it.
In a run with the Red-Tail, which I am still doing but have saved because I needed a break, I got my grubby little hands on a Fire Beam. After running around to get enough scrap to buy it, and then running around to get enough scrap to power it, I have simply been taking down shields with one or two of my Basic Lasers and setting everything on fire. This is hilariously effective and has taken down every ship I've encountered since without destroying it.
update: I later got a Burst Laser I and Heavy Laser II, alongside two Automated Re-Loaders. Using these, I breezed my way to the flagship, incinerating everything in my way, took down its first stage, and promptly died horribly to its drone swarm.
In a run with the Kestrel (remember that old thing), I picked up a few mantis and put them in my oxygen room. I then encountered a ship with 3 zoltans, a human, and a two person teleporter. A human and a zoltan teleported onto my ship... in the oxygen room. Let's just say they did not have a fun time.
"I can't prove it, but I can say it." -Stephen Colbert