Ultimate Weapon Stats (Official v1.1 numbers - not like it has been changed since release):
Doom Ray:
Size: 10 + 4% of ship size
Damage: 22 (Beam)
Cost: 150
Black Hole Generator (Blackhole Gun's weapon)
Size: 6 + 4% of ship size
Damage: 16 (Gun)
Cost: 100
Blackhole Eruptor
Size: 11 + 2% of ship size
Damage: 25 (Missile)
Cost: 160
Okay, if you're not good at math, I'll go ahead and do it for you. Keep in mind that this first part is only size versus damage.
Analysis 1 - Doom Ray vs Eruptor
At size 24 and smaller, Doom Ray is 1 size smaller than Eruptor. At size 25-74, Eruptor is the same size as Doom Ray, but deals 3 more damage, and is therefore better. For any ship with size 75 and above, Blackhole Eruptor is clearly the best weapon because it will be smaller and do more damage. If you get maxed miniturization on a huge hull and get 200 hull space (not accounting for hyperion shinkers), Doom Ray is actually 5 spaces bigger than an Eruptor.
Analysis 2 - Doom Ray vs BH Gun
Blackhole Gun is consistenly 4 size smaller than Doom Ray at all ship sizes (since the size mod is the same), but it also deals 6 less damage. If you take that into consideration, then as long as the 4 spaces makes up for 6 damage, you're better off using Blackhole Gun. In this case, that means a anything less than 124 spaces. At 124 and smaller, both Doom Ray and BHGun adds 4 to their size (because it rounds down - or is suppose to), making doomray 14 size and BHGun 10 size. A little cross multiplication and we see that 14x16 = 224 (14 BHguns at 16 strength), and 10 x 22 = 220 (10 DoomRays at 22 strength). If we go further than that, 15x16 = 240, and 11x22 = 242 means that DoomRays are better. So in this case, if you have 0-124 spaces on your ship, BHGuns are better, and at 125 and above Doom Rays are better. (Note that the end number is just the value recieved when you cross multiply the size and damage. It only reflects how valueable the weapon is in those aspects, not how much damage a ship can deal using those weapons.)
... BUT, we already know that Erruptors are better than DoomRays at size 24, so that means...
Analysis 3 - Erruptors vs BHGuns
The relationship between Erruptors and BHGuns doesn't have clear cut numbers that we can easily see. On one hand, Erruptors does 9 more damage, is 5 sizes bigger, but on the other hand, that size difference reduces as the hull size goes up. This makes the formula a little more confusing because you have to also take into account the size changes...
Let's start at hull size 99, BHGun is size 9 (6+3), Erruptor is size 12 (11+1). At this point, 9 x 25 = 225 (9 Erruptors at 25 strength), and 12 x 16 = 192 (12 BHGuns at 16 strength). Erruptor wins here, and thus any hull sizes above that and Erruptors are better (because the size difference reduces, but the damage difference doesn't).
At hull size 49, BHGun is size 7 (6+1), and Erruptor is size 11 (11+0). Here, 7 x 25 =175 (7 Erruptors at 25 strength), and 11 x 16 = 176 (11 BHGuns at 16 strength). BHGuns wins here by one point, but that means any hull sizes less than 49 and BHGuns are better.
So we hit the middle mark of hull size 74, where BHGuns are size 8 (6+2) and Erruptors are size 12 (11+1). There we see that, 8 x 25 = 200 (8 Erruptors at 25 strength), which is still better than 12 x 16 = 192 (12 BHGuns at 16 strength).
Anotherwords, for hull size 0-49 Blackhole Guns are better, but for hull size 50 and above Blackhole Erruptor rules the day. Doom Ray doesn't even compare to these two weapons when it comes to size versus strength.
As for production cost analysis (cost per damage first for simplicity's sake because size changes on different hulls):
BHGuns: 100/16 = 6.25
Erruptors: 160/25 = 6.4
Doom Ray: 150/22 = 6.82 (6.81818181818.... actually, but eh...)
So yeah, Doom Ray is dead last here as well.
Oh, what the hell, while I'm at it... (cost versus size)
At 24: 6 x 160 = 960 (6 Erruptors each cost 160), and 11 x 100 = 1100 (11 BHGuns each cost 100)
At 49: 7 x 160 = 1120 (7 Erruptors each cost 160), and 11 x 100 = 1100 (11 BHGuns each cost 100)
At 74: 8 x 160 = 1280 (8 Erruptors each cost 160), and 12 x 100 = 1200 (12 BHGuns each cost 100)
At 99: 9 x 160 = 1440 (9 Erruptors each cost 160), and 12 x 100 = 1200 (12 BHGuns each cost 100)
So what does that say? It says Erruptors ends up being real expensive really quick (especially because you can put more of them in). (Note again that this is just a cross multiplication of the size of the component and their cost, not how many you can fit on a ship and how much a ship will cost.)
So... after all that:
Why use Doom Ray? It's the fastest weapon to reasearch because beam weapons techs are cheap. As a result you will be able to get it faster and will hopefully be able to smack your enemies BEFORE they get better weapons than you. It is also more efficient in larger ships than BHGuns, and that is important because your ships will be pretty big at the end.
Why use BH Guns? It's cheaper and especially good for smaller vessels. Its small size allows you to fit in more of them when you might not be able to fit the others. While there is definitely a disadvantage to using it than Doom Ray, if you rushed for Nano Rippers already, you might as well stick with it, because it isn't necessarilly terrible either. It is also cheaper than Erruptors to research.
Why use Erruptors? As the end game weapon, it is clearly the best weapon around. If you can afford it.
Hope that helps somebody...
