Now this is rarely the case in Hard AE, but sometimes the games throws nice stuff at you. I already had several good sets of weapon combos available when I came across a store that carries Halberd and Fire Beam and Swarm Missiles. This is sector 6, I've got about 6 jumps left.
Which combo would you take for a) going to the final battle and b) for each flagship phase?
I was very partial towards taking the Halberd Beam and swapping it with the Anti-Bio Beam, as it increases damage per second significantly - however, it will not allow for easy crewicides and (I think not by much, but still) decrease scrap rewards and thus lowering the all-important score

Considering the first flagship, I'd go for the Fire Beam to eradicate most of the enemy crew and also conveniently damage systems, and I could still keep the Breach I. The Breach II is much better than the I, but also takes two power bars, so is not so combinable with the available weapons. I'd want to keep the Vulcan and the Dual Laser, so three weapon bars are left to distribute. I also like using the Hull Laser I with the Breach I to maximise the laser barrage and still do a little breaching here and there, but it's also not so useful for killing off crew.
So what would you do?
I haven't decided yet, but after lengthy considerations I lean towards keeping the Anti-Bio Beam and the Breach I equipped, maybe swapping the Anti-Bio with the Hull Laser I in phases two and three.