I’ve been less than impressed w/these modules. Am I using them incorrectly? Here are my observations:
Sheild Support Beam 1: Doesn’t always fire.
Crusier Camouflage Shield: Never seems to deploy unless it doesn’t need to, or it is too late.
Repair Systems: Often are less than half used when ships explode. Camouflage Shield doesn’t seem to fire at right times.
Repair systems are great when you’ve got enough armor to stop enemy hits, but still need to repair lucky hits. Without a repair system the lucky hits will pile up and get your ship destroyed.
So Repair Modules are basically used against fighters?
Unless things have changed, the general consensus here in the forums on the Camouflage Shield is that the only race that gets any benefit from it really is Tribe, due to the high HP value of the module. And even that isn’t enough to make people use it.
You could also use them on a weaponless “fighter carrier”, but I guess it’s better to put an extra armor plate in this slot… unless you use Tribe.
The Shield Support, or ISSB, was intentionally nerfed hard after serious abuse in 1.44. Since then it has become useless.
Camouflage is useless in it’s current form for too many reasons to list. Let’s just say it’s something you won’t put on your normal ships even if it’s free. And cost way too much for HP tanking, even for Tribe.
Repair is used when combine with armor tanks. Otherwise it’s useless.
Speaking of Tanks, how do you build them? I tried an Empire Cruiser with 13 Heavy Armor, but weapons could still hit it. (I had an engine/weaponry on it.)
Speaking of Carriers, only ever playing missions, I have never needed more than two fighter repair bays. Does this sound correct, or should I use some slower fighters with more bang that will get hit more?
[size=150]Useless cruiser equipment[/size]
* EMP Shield. A noble idea, as being hit with cruiser EMP beams or (much more commonly) frigate EMP missiles is a good way to get killed. However, the counter is highly ineffective because the blocking modifier is too weak. You’d need about four of these modules to have a good chance (not even a guarantee!) of being proof against all EMP effects. Alas, even the ruinous loss of that much hull space from such a strong installation is useless because of the excessively strong stacking penalty. I find it simpler to beef up my Guidance Scramblers (and deploy escorting frigates at greater range) to knock dowm EMP missiles instead. It’s not worth allocating precious multiple slots for a counter that is actually mostly absent.
Target Booster. Like with the Point-defense scanners, these boosters add very little to the tracking of your weapons. Even the type II booster is weak, despite allegedly being 60% stronger than the type I. Better still to choose your offensive armament intelligently and put another system where you’d be tempted to try a target booster.
Carrier Bay. The reinforced carrier bay is superior in every way, and for only thirty credits more - a trivial increase in cost. On a multi-thousand-credit warship, I’m not going to argue about a cost difference on the order of 1% of the ship’s total price. The reinforced version gives me 100 more points of repair supplies, and a whopping 50% more hit points. It even requires only one more crewperson, too. Don’t waste your time with the basic carrier bay.
Proton Beam. The cruiser beam laser, while comparable as an armor-busting energy weapon, definitely justifies its higher price. How? The proton beam has abysmally poor tracking, a long rearming cycle (even among other slow-to-load weapons), greater weight and less damage output. Penetration stats and optimum ranges are closely comparable for both weapons,but it’s very hard to justify using proton beams - despite their budget price - if their aim is so much worse. We all love weapons that rarely hit, right? One might make a case for using the proton beam if you’re aggressively “pinching pennies” during ship design, but in most cases it’s a waste of a slot. I didn’t come here to play “Gratuitous Budget Battles”. 
Quantum Blaster. This is something like the excellent frigate Ion Cannon, but for cruisers. It’s unfortunate that it didn’t scale-up closely enough from frigate size to fully deserve that comparison; the Cruiser Laser is a much better example of such. Its tracking is fairly low for something that tries to fit in among low-damage but high-precision weaponry, and it’s somewhat slow to arm as well as a bit weak in damage output. Its only real advantages to me are very low power requirements and a cheap cost. If you’re looking for a choice to fill your final weapon hardpoint after meeting your design requirements for a mission, the Quantum Blaster is a decent choice, as it’s better than nothing. However, that’s a mighty slim case to make for using it when so many better choices exist.
My carpal-tunnel pain is wrecking me (despite the great amount of time I took to type this post), so others should now add to the “waste of space” list if they like.
Thats a great list, Archduke Astro. Has anyone ever added to it? I had questions about the EMP shield, as my ships always seemed to get hit anyway! It’s sad to hear about the Target Booster. When you say “beef up” Guidance Scramblers, do you mean add more? Do you find the Frigate Point Defense MK’s a waste also? Do those hit fighters?
Thanks. 
Pt. Def. guns never affect fighters; only physical seeking wpns. (msls., rkts, torps.; not plasmas).
Yes, I meant add more Guyiance Scramblers. I typically use 1 on each cruiser; 2 if that design’s a major part of my strategy. A “picket line” ringing yhour fleet core, using cheap cruisers with no main anti-ship guns but with 4 GS’s each, can be costly but highly effective.
For frigates, PD is the only game in town for countering seeking wpns. On a single ship-to-ship basis they’re OK-to-mediocre, but even just 1 or 2 PDs per frigate, multplied by dozens of frigates operating in careful formations, can nearly missile-proof your fleet core. That is, until dedicated frigate-busting cruisers ( or rkt. + painter fighters ) ring your doorbell, though.
I got so sick of the official EMP Shield that I modded my own. It’s purposely not 100% effectve, but it’s way better than 3 or 4 vanilla ones all asleep on the job.
Keep asking such good questions–very useful thread. Really gotta leav the keyboard now though; sorry but arms r screaming. 
I have such a huge list of useless items that I better off listing just what’s useful than what’s useless.
But Photon beam is definitely NOT useless. The difference between 73 armor piercing and 70 armor piercing can easily be 3000+ EHP. You want at least 1 in a fleet to bring tank armor down to 70 for normal beam lasers to finish off.
I wouldn’t mind a “what’s useful” list!: 
I basically just use a bunch of Fast Missiles and one Proton Beam on my cruisers. Get rid of the shields, and then when your close (the AI of the enemies always brings them close), the Proton beats down the armor the fastest. I don’t think I’ve dealt with Tanks, so a Cruiser Beam Laser might be a better choice, but since I only play missions so far, I was going for the highest Honor I could get, Proton was cheaper, so Proton it was.
Repair modules work alright on Tribe ships, given how fast theirs repair and how beefy the ships are; everyone else usually dies too fast for them to be too useful, unless it’s an armor tank.
Then I’ve simply been fortunate to have not encountered that kind of tanking abuse in my gaming, then. I haven’t suffered from the lack of the rather clumsy & inefficient Proton Beam, and I’m grateful. I’ll gladly concede that it isn’t useless, but only as long as one is facing known (or strongly suspected) armor tank-loaded forces.
I agree that the list of what I’ll charitably call the most useful equipment is a lot shorter.
Oh, photon beams are clumsy and weak, no doubt about that. They are more of an utility gun that you have about 3 in a fleet of 90000 credits to help break armor tanks, which tends to have a defense between 77 - 81.
Also, photon beams hit a lot more often than plasma does simply because they are beam types, and has no problems in hitting slow cruisers. Unlike Plasmas and Missiles, beams does not have the “move speed too high -> reduced hit rate” problem.