I've done some work looking at average WMD per second for all non-launcher weapons in 1.6.3, and there's some interesting stuff there. First off, here's my assumptions:
1. All shots in a burst hit the target
1a. The game isn't lying about how particle hit detection works. (It's wizardry we don't quite understand yet)
2. No round-off or damage resistance is encountered, nor any bonus applied.
3. Every hit does exactly the average damage
4. Passthrough weapons (just the katana in this graph) don't.
5. The wiki values for what % of damage is done by each WMD category are accurate
6. WMD0 weapons do 1 point of WMD on each hit
7. When WMD weapons have less effective WMD than their rate of fire (thus, less than 1 WMD in average damage) this can be safely rounded up to 1.
8. Fragmentation weapons use their damage as calculated by the game's stats system. This is not especially accurate and I may redo the graph with revised totals to fix this. As it is, fragmenting weapons (Urak Howitzer, Kiloton Cannon, etc) are likely to do quite different damage to what's shown here.
Here's the graph I got at the end of it. Trend line is for all damage types.

(I would put it in spoilers, but those don't work)
A few things strike me immediately:
-Thermo is all over the freaking place, to the point that it's messing with the trend line
-Laser WMD/s trends downwards over levels, because rate of fire decreases and no WMD is applied.
-Against a WMD target, ignoring resistances (again, I don't know if armor resistance applies to WMD, but I suspect it does) the QAC actually does better than a Lamplighter. If you can hit, which is the main issue with the QAC.
-Particle weapons only really include one decent WMD weapon, the Nandao bolt cannon.
-The Mark VII howitzer is basically an APA, one level earlier. Theoretically at least: in practice damage resistance will make it less effective. Still, it's a joint-first place for those two weapons on the WMD/s front.
-Worth noting: the penitent cannon theoretically out-damages the Chimeric Graviton cannon against capital ships. It's 2WMD/s compared with 1.5. Wow...
Also immediately obvious: the Mark I howitzer sucks. It's out-performed by the supposedly worse AK505.
In the wider picture though, we need to work out what's actually wanted for WMD. Right now, it's a necessity. Internal compartments are really, really tough, and you basically want as high a WMD-rated weapon as you can get. Making the weapons balanced against internal HP that trends upwards by level would mean making a much simpler graph with a far clearer (and more linear) trend. However, this would reduce the value of howitzers and make a lot of weapons very samey. I don't really have a firm suggestion (although I'm tending towards thinking that WMD should be a "bleedthrough" effect: things take normal damage from everything, but WMD weapons do their WMD damage through armor to the compartment underneath what they hit....so they kill things faster but without crippling the other weapons), but it's clear that WMD-average and WMD/s needs to become a more common measurement of weapon balance, both in the community and in the vanilla game.
Edit: Oh, and if anyone wants my spreadsheet, or wants me to post the raw numbers then I can obviously do that.

Edit2: Tweaked my assumptions to be more accurate, fixed a problem with the AK505 (WMD was set to 1 in my sheet, not 5). Thanks to NMS for pointing this out.