I played around with anti-fighter cruisers a while ago, against ~1000 fighter swarms of Rebel Icarus laser fighters at ~2.68 speed. For non-mod factions, excluding Parasites, Cruiser Defense Lasers (CDL) are about the best you can do, using 6-8 on a single cruiser, 1-3 repair modules which can fix armor, and 2 or 3 plates of armor (enough to get over 8 average; higher is better, of course, since it gives the repair more time to work) and a shield with enough resistance to bounce fighter lasers (shields do a considerable amount for cruiser survivability against anything). 5-7 Cruiser Pulse Lasers (CPL) with one or two tractor beams (TB) work next-best. Against those 1000-fighter swarms I was playing with, I’d see a victory with roughly 12 cruisers armed exclusively with CDLs, as compared to roughly 18 cruisers with CPLs or CPLs and TBs. Interestingly, against laser fighters the CDL cruisers performed less effectively when I added TBs. Not certain about the CPL cruisers, because it’s been a while since I tried it. Also note that the exact numbers of cruisers will change based on which races you play with and what weapon load-outs you choose.
As for why I excluded Parasites: against a ‘true’ fighter swarm, the Parasite’s Flak Cannon is a wonder weapon. I mentioned that I needed 12 cruisers with 8 CDLs each to kill off 1000 Rebel Icarus laser fighters. Using the same hull (Physalia) and replacing seven of the CDLs with Flak Cannons and the last with either a Tractor Beam or a Supercharged Tractor Beam (I don’t remember which, though I suspect I used the standard version), I was able to win about 2 out of three attempts with just two such cruisers against the same ~1000 fighter swarm (this is true post-nerf for the Parasite Flak Cannon (CFC); pre-nerf, I wouldn’t have bothered with the TBs, and I think it would have been more like 100% of the time on the win-rate), though I usually lost one of the cruisers even in victory. Always remember when using Flak Cannons that you either need to keep a safe distance between your ships, or you need your ships to have enough armor that the splash isn’t killing them.
As for why I might choose any particular weapon over the others:
CFCs don’t play nicely with lightly-armored ships. This means that they can be a blessing against huge fighter swarms, but they can also be a curse when they start killing your own fighters and frigates, or your lightly armored or damaged cruisers. I prefer not to use them unless I know I’m going to see large numbers of fighters or frigates (preferably both) in the opposing fleet. If you want to use these as a primary fighter defense, you need to have tractor beams or you need to only need something to hold fighter groups down; the primary role for CFCs is either going to be as a frigate-killer, as a counter to true fighter swarms, or as an anti-ship weapon that also happens to kill close escort fighters around the primary target (and no, you can’t use these to clear the way for your own strafing groups unless you’re really careful with target priorities and very lucky, because the splash will kill your strafing groups at least as effectively as it kills close-escort fighters).
CPLs are primarily an anti-frigate weapon, with the potential to hurt cruisers once their shields go down (unless it’s a heavily-armored cruiser) or swat fighters more effectively than the heavy cruiser weapons can. As an anti-fighter defense, I prefer to use them on a one-per-cruiser or one-per-bait-cruiser basis, depending on fleet size and design. The minimum range on the CPL hurts its ability to defend the cruiser carrying it (in fact, if you want your cruisers to defend themselves, CFCs and CDLs are by far the better choice), but the maximum range means that a moderate or large cruiser group carrying these can bring a lot of fire to bear against fighters. Unfortunately, this same higher maximum range means that it’s more likely to have high-priority targets (meaning cruisers or frigates) in firing range, so it will shoot at those instead of the fighters swarming around the fleet. The CPL also needs to have support from TBs to be really effective as an anti-fighter weapon, though unless you feel like it you probably don’t need this to be a 1-1 ratio.
CDLs in my opinion are the best dedicated stand-alone cruiser-mounted anti-fighter weapon in the game for anything except excessive fighter swarms (for that, use CFCs). However, most frigates won’t be hurt by it as long as their shields are up (unless someone isn’t using shields and has a very lightly-armored or unarmored frigate), its short range makes it very unlikely to be able to contribute even to finishing a cruiser (and it certainly can’t hurt the majority of healthy cruisers), and it lacks sufficient range to support anything but a closely-packed fleet for group fighter defense. Still, for space efficiency it’s good - it doesn’t need a TB to become particularly effective, its lack of range helps keep it focused on fighters since those and fast frigates are the ship-types most likely to engage at very short ranges, and it’s relatively cheap. Unfortunately, there are also cruiser hulls which are large enough that the CDL can barely reach the other side of the shield bubble, so it might only be firing at fighters which are already strafing the hull.
TBs are interesting for anti-fighter purposes - they don’t kill fighters on their own, but if they catch a fighter, they can slow it to the point that even main battery cruiser weapons are not terribly less effective than CPLs, CDLs, or CFCs (the low fire rate on most main battery weapons, however, still means that the CPLs, CDLs, and CFCs are generally superior, and the higher tracking for these three weapons also helps as long as the fighter is only slowed rather than stopped). This means you need another weapon system to pair with your TBs. This could be escort fighters (even unpainted rockets will work against fighters caught by TBs), cruisers with CDLs/CPLs/CFCs/Quantum Blasters, or similar, frigates with Frigate Pulse Lasers or Antifighter Missiles or Ion Cannons, or an ‘ignore until main battery has nothing better to shoot at’ policy (best paired with armor and repair), or something else. I personally feel like squadrons of escort fighters are the best pairing, because nothing else gets you as many guns for the same cost (fighters are roughly 1 gun per 80 credits, most cruisers and frigates are more like one gun per 200-300 credits), and on top of that fighters have some of the fastest-firing weapons available, though if you’re going to go in for an escort squadron for every cruiser you might as well just try for fighter superiority on the map. After that would be a mix of CPLs or perhaps CFCs on some cruisers and TBs on other cruisers. CDLs often lack the range to pair with TBs on other ships, and besides which are effective enough against fighters without TBs.
Some Anti-fighter Tactics:
Bait Fighters - fast fighters intended to lure enemy fighters off to who knows where. Only works if your opponent has set fighters to engage other fighters, and depending on ranges and other orders (e.g. rescuer) may also need to have a higher priority for attacking fighters than for attacking frigates or cruisers. These can be unarmed, but if they don’t carry a real weapon they will often be ignored in favor of something more dangerous, so rockets tend to do well here.
Dogfighters - if you think you can get a better fighter force than the enemy has without hurting the rest of your fleet, you might as well obtain fighter superiority or supremacy on the map unless you want to spare the budget. This can be local, in which case you want to use escort orders, preferably on something that can contribute a little to the dogfight and which is likely to draw enemy fighters to it, or global, in which case you’ll be allowing your fighters to range freely across the map (note that attempting global fighter dominance is unwise if you’re on the posting side of a challenge - you can always figure out a way to exploit the targeting or driving AI, or come up with a better group of fighters, or set up traps when you have the advantage of being the one attempting a challenge, and a large fighter force that can be drawn off or broken easily is a significant investment that will likely do nothing for you). This might turn into your own fighter swarm, however, and if it does you need to make certain that your fighters are the better fighters.
Anti-fighter Tanks - basically a heavily-armored cruiser or frigate intended to simply endure fighter attack. Best to include shields to reduce the number of hits on armor, which reduces the frequency of ‘lucky’ hits which hurt armor. Also should include something that can repair armor, and a weapon so that the attacking fighters don’t lose interest. Often good as a core ship for local fighter dominance strategies, in which case you might also play with carrier modules (though I’d rather spend the credits on more weapons or more fighters).
AA Ships - ships with lots of anti-fighter weapons. Work best if they can draw enemy fighters to them. These are also good for the core ship for local fighter dominance strategies. These are what I was playing with in the tests described in the first section of this post. Frigates with anti-fighter missiles work well in this role, especially when TBs or painter fighters are involved, as AFMs have the range to support most of the fleet. Note that AA ships either need range or numbers if they can’t draw fighters to themselves, and should probably be deployed in areas of the fleet where they can protect as much of the fleet as possible (this can be off to the side of the fleet, if they can draw the enemy fighters off in that direction, or it can be in the center of the fleet so that their guns cover several nearby ships).
AA Weapon per X Ships - spreads out your AA, making it less likely for you to have a significant loss of coverage, but also making your fighter defenses less capable of dealing with any one ship being swarmed. I usually use some variation of this.
Fighter Escorts - cheap fighters deployed to shoot at strafing fighters and given orders which keep them close to important ships. This can be a local-superiority dogfighter defense, but usually for me it’s more of a ‘draw some of the enemy fighters’ fire and try to kill a few while doing so’ kind of thing. Rockets work if you have painters or TBs or don’t care how quickly enemy fighters die as long as they aren’t shooting up your cruisers (probably meaning you went for the ‘draw enemy fire’ variant of the escort fighter), lasers or painted rockets are somewhat better but cost more than just rockets. Painters work if you’re using a missile for anti-fighter duty (meaning you have anti-fighter frigates or rocket fighters in your fleet, excluding mods), but like lasers and painted rockets tend to cost more than pure rockets.
Sufficient Armor - put enough armor on your ships to make them stand up to strafing for a while and hope for the best. This can mean a focus on killing the other guy’s cruisers and frigates fast enough that you win before the fighters break the armor on enough ships to matter, and is a good idea with any form of anti-fighter strategy. If you’re going for the ‘ignore fighters and hope for the best’ variation of this, it’s better to bring ship armor up to around 20 average (perhaps higher) to give your ships a bit of leeway before lucky shots break the armor. This variation leaves you vulnerable to fighters and fast frigates (since fast frigates are mostly countered by the same weapons that you’d use against fighters), but depending on opponent fleet composition could allow you to destroy the main portion of the enemy fleet quickly enough to claim victory without needing to deal with the enemy fighters. Sometimes it works and sometimes it doesn’t. All of the other anti-fighter strategies should be combined with some minimal form of this just to avoid module effectiveness losses due to strafing damage, even if it isn’t enough armor to bounce fighter lasers.