What is the weapon of your choice, and Why?

[AgentZero]

My personal favourite would be a few sets of shield disrupters, then WMGs, then APBs. If a ship's got any shields left after a the SDs, the WMGs take care of that, and the APBs finish the job.
As for missiles, I'm play with a self-made mod where they are a lot more powerful, and also have their own set of mounts. A Massive Mount CSM will take out a Dreadnought with 1-2 hits.
But in the stock game, I only ever used missiles as a support weapon. I'd have a squadron of BCs usually, loaded to the gills with CSMs who would hang back and pummel the enemy from afar. The AI (and most players) doesn't put enough PDCs on their ships to deal with seriously heavy missile bombardment so they'd have to use other guns, and each one of those fired at a missile is one NOT fired at one of my ships. :-)
I also find a few CSM ships quite useful for bringing down Starbases. It can sometimes take a while but it keeps my ships out of the way of Massive Base Mount WMGs, coz those things hurt!