I also find Squalls to be pretty good weapons, with the caveat that I usually don't use them against my main target. Instead, I find an enemy that is under pressure from other friendly ships and launch a missile volley at them. A full Squall volley is enough to tax even a Paragon's flux capacity, and when a ship is already trying to defend itself against a different cruiser the added damage can be back breaking. They're like a kinetic Pilum volley that never ends. I can't tell if they're my favorite large missile (none of them really excite me, but I've never played with Missile Spec 3), but they serve a definite purpose.
And nobody mentioned my favorite missile of any slot size: the dual Atropos torpedo rack! The trick is to think of them as heavy Harpoon missiles rather than guided torpedoes. They're like Hammer torpedoes with enough guidance to always hit anything of destroyer size or larger, and a well timed shot can even nail a frigate. They come in a rack of two as opposed to the three-shot Harpoon missile rack but can deal WAY more damage per hit, and they're beefy enough to bypass light point defense screens that would stop most small missiles. I often find myself wishing there were medium and large Atropos launchers for high explosive death in larger volumes. Other small missiles all have their niches, but if I don't need a specific other kind of missile for a given ship I usually slap on an Atropos.
Last in my list of unpopular weapon opinions, I honestly think the autopulse laser is my favorite large energy weapon because of a very specific synergy. As mentioned previously, the APL suffers from low sustained damage output unless it has extended magazines. Do you know what else likes extended magazines? The best PD available to high tech ships, the burst laser. With the three of those things combined, you can get great burst damage while being incredibly safe from fighters and missiles. And while plasma cannons have the best damage over a long time, the burst from a couple extended magazine APL is ferocious and will leave most cruisers overloaded with a hole in their face. But most importantly, I love the APL sound quite a lot. The plasma cannon is amazing too, but if I'm looking to give a ship high burst damage and better defenses, I'll usually pick the APL over plasma.
