I'm talking about PvE, where module sniping is not needed.
Let's take a combat ship like the gunship or the Fer-de-Lance. I've tried several weapon loadouts on those ships and by far the most destructive weapons are multicannons. I've tried full lasers, a mix of lasers and kinetic weapons, special weapons like plasmas or rails, but nothing comes close to how fast ships get destroyed when using multicannons.
I have both of those in main line-up of four, and don't
quite use all multi-cannons. But you might be right that I should, at least with engineered Incendiary weapons.
On the Gunship I like to have two small railguns. That ship has enough mass, power and overall firepower that it trivialises the disadvantages of just two small railguns, it makes me feel a little less useless when chaff comes out (I use gimballed multi-cannons on it), it's really not bad at sniping when you target a sub-system to get a smaller reticule over the target, and once I engineer them, they'll disrupt shield cell use.
On the Fer-de-Lance I wouldn't dream of giving up my huge fixed beam, and not just because I don't like the look of huge multi-cannon fire. It's a great little fixed sniper, and the way I fly the Fer-de-Lance I really can't stand risking running completely out of firepower. Beams have a great damage profile, are vastly improved by engineering, and complement multi-cannons really well.
Still, multi-cannons are probably the best weapons out there if you use Overcharged, then a mix of Corrosive, Incendiary and no-special-effect.
I also love crazy loadouts, specially on small ships, and I'd love to build a true missile boat and a ship similar to those Cluster Flak Arrays and Flak Artillery Arrays builds on X3.
I've been working on a relatively 'crazy' loadout for my other two main ships, my Clipper and my Courier. It's... not entirely succeeded yet.
With the Clipper I'm trying to build a laser artillery ship, with the Long Range upgrade's brilliant advantage of essentially no damage fall-off. Haven't quite got myself comfortable with it yet though: fixed beam on one wing is a given, the rest gimballed is too, but I'm playing about with pulse/burst, struggling with the distributor a bit, and am still considering using an Orca instead simply so my symmetry obsession isn't frustrated.
The Courier I've been flying with three flak cannons, aiming for all Double Shot, one Corrosive, one Incendiary, and one Drag Munitions. I tried it briefly in beta with heavy engineering and while it took some getting used to, it was a hell of a lot of fun. Not really a RES/CZ ship except that my Courier is also my surface prospector, and
eventually I'm going to have enough raw materials for synthesis, right?
I did also try all railgun and all plasma accelerator Couriers, but... no. Nope. Just no. Railguns fry it too badly, Efficient plasma accelerators kind of work but don't give enough of a damage boost over 2 MC / 1 beam to justify all the trouble, Focused plasmas are easier to hit but really have
no damage advantage over a more basic build and put far too much strain on the distributor, etc.