Also thanks to everyone writing, this thread is really helpful and nice to read 
Translation: "The Nerf-Hammer is Back in Business, Baby!"
But yeah, this has been a very informative thread, and I've been slow to chime in. It has been great that some of the weapons touted are ones I never use (nerf gun, etc), and this goes to show the richness of the diversity that Dioxine has built into this mod.
Some general thoughts.
Bows:
In my recent play, I have stepped away from bows entirely. Early scale mail gals benefited greatly from them for early stat growth and were a solid core of my early game cadre. I think the hunting bow is my preferred weapon in the series. The ability to get off three shots per turn is terrific, and sniping over the Airbus/Car/Pachyderm is a great tactic. I missed the ability to use fire arrows, but that just made these even better imo. (Btw: how about the ability to make agua arrows for the combat bow say after Chemistry. These require Chitin as the arrow heads would be fashioned from Lobster shells, and impregnated with some caustic chemical (maybe it causes a bit more morale damage too)). The longbow suffers in its time restraints and with my play only gets off about a shot per turn, with that shot often not dropping the target. I know Meridian is still using these as a stable weapon in his fairly homogenous arsenal and they are working well for him, so its probably just my playstyle that puts me off them. I will say that my impression of bows was probably heavily influence by the "its practically impossible to hit things on the diagonal" bug that I believe should be resolved now. In my next run I'll give these more of a try. And also, I'm a believer in the Future Bow but haven't been fortunate enough to unlock them in my current run.
Pistols:
Early game I love the Black Marches!! Nice ammo capacity, fairly common (decent ammo resupply) and that 2-shot auto is great for the upclose "crap, my handle missed, I'll try to take this guy down with my last remaining tu's" moments. The holdout has been useful in early skimpy outfits for last gasp efforts and also some general marksmanship practice. I pretty much avoid all other pistols as too underpowered after this, until I get the Smart Pistol. These are terrific weapons, and everyone gets one for a good chunk of mid game. Perfect for reaction training on Scorp Hunts.
All the self powered lasers are terrific, with the Scorchy becoming an excellent side arm in mid game/late game. It can breach mansion walls, so makes a great tool there.
SMGs:
Early on, anything can be good. Assault SMGs were very solid for me, with nice hits as decent ranges, and the burst great for up close finishing. Blackmarch is nice too. However, the SMG with its 2X1 is great. With the advent of Incendiary munition, this becomes a staple for my squads. Snipers get them for the first steps to the roof of the bonny. They can auto fire at enemies spotted, but they are also great for lighting up night maps. Burst fire upclose with incendiary is often a terrific finisher, and this is a solid side arm for all of late early through mid game. The new addition of the Spikey looks awesome too, but I'm not sure how often I'd chose the melee over an autoburst if I was serious about downing someone. I think the Linux branch is really cool and I like the Origami's melee hit sound. The Deathblossom with API is a solid favorite for many of the reasons above and is often kitted out with my Shield basher. I put one of these gals on the Jetbike and soloed many civ traffic runs, as well as the early game missions, (tower, outpost, rodeo, warehouse, etc). API lets me light up the terrain, and takes down foes quick, and because its a one-hander there is no aim penalty. I used it so much, I created hand sprites for it to enrich my play. The king of SMGs however, for me, is the Cougar. As soon as I can, everyone gets one. It only needs 2x1 slots so it becomes the new Pistol for Everyone. Except its not. Not a pistol. Its a hungry, death spewing, instrument of mayhem and carnage. I just gave my new "Mansion Express" crew a workout with these. The auto shots reliable chew through mansion wall, and I took down many foes by targeting them through the walls and letting them rip. With the first couple shots taking down the walls, I'd often get a hit or two with the remainder of the burst. Time costs, good aim, decent ammo capacity. These are just so solid. In the mansion run, I ran out of ammo a few time due to my flagrant use of them to breach instead of using my rippers, but I carried a reload for everyone so this was never a problem. As far as energy/higher tier smgs: The XG Assault seems nice for its snaps, but at 3x1 it feels like it competes with rifles in this slot. Ret Plasma guns have been great for dealing with early mercs for me, and the assault laser is a great weapon to pick up in early pogroms as an "in battle upgrade" if you run across them. The plasma subrifle is nice if you can unlock it early, as it can also be a nice merc counter.
Rifles.
Hunting rifle/scoped rifle/ scoped carbine. All terrific for early game. Once I get PS ammo, the Battle Rifle becomes the main staple in the arsenal. Anyone who isn't specialized gets one. Good aim, good stopping power, gun butt attack for stunning, its just such a solid fire arm. Great for early game, and into mid game. Of course all of the previous discussions of Gauss Muskets are dead on. Its deadly, its lovely, its solid. I often up-gear to it for those "tougher missions." The Smart Rifle is solid, but I find I've often specialized my crews out by that point, and only have one or two "general troopers" that might use it. I pretty much ignore lasers until I can get the self powered versions. Looted Stingys from Siberia were solid for a good part of mid-game. Very nice range, hits often. I've never messed with the Eurolas-rifles, put off by their price tag, but they look solid. I know one player who rushes for them in early game then uses them to dominate. I like the idea of the XG Rifle, as I can supply my own ammo, but I haven't used them much. Of course plasma weapons, once available become terrific in their own right.
Sniping systems.
The good old sniper rifle is a terrific weapon. It only gets replace by the Custom Snipin Gun. Two rounds, are twice as juicy. I almost always use this mode with these weapons. My feeling is that the first round may not kill, but it may do enough Armor damage to let the second round finish. This may not be born out in actual game mechanics, but that is what I like to imagine in my own head cannon.
Sniper Gauss: Awesome. Its the up-gun for snipers for those tough missions. I've worn down tanks with these, downed many power armored foes too. Its draw back: Overkill.
I'm just bringing some Bossars online to play with their auto fire, so that should be fun. So far, I've not run into any Energy weapon systems that I consider a good sniper tool. I've used a stingy as an alternate for my snipers (ie, scorp hunts, etc) but nothing as a main gun.
Heavy weapons.
There is little so satisfying as firing your HMG through 4 shanty buildings to vaporize a rat on the other side of the map.
The penetrating power of this tried and true system is often worth the hassel of getting into firing position the turn before. The Heavy Gauss is a great counter to Power Armor, especially when the muzzle is placed in the backplate immediately before pulling the trigger.
I love grabbing these as battlefield loot, and running around with them. Just drop them at the end of the turn if you are over burdened. Auto lasers, are nice for the same reason. The Fatty, is a great tool once you get it. 20 round bursts shred terrain and foes alike. Not a fan of the Heay Laser other than for parts. The mortal is solid, but I not employed it recently. The 90 power felt like it often left heavy targets (tanks, power armor) still up. The other place I'd look to use it is clustered enemie: great to knock down 3 at a time, but typically I play on medium difficult and I don't often get that target density. The tornado is a great alternative but its so heavy I can't even use it right now.
RPG/Rockets, etc: Panzerfausts are really king for a long time. I do like the quad launcher at times, but have not had the bravery to employ the dragons much. As far as the Advanced Launcher goes, what I really want it to do is have two waypoints. This will come when the OXCE version catches up to the nightly a bit more, as this is in the main branch. (As a side note, this will make the Sentry Gun a viable tool as well). The recoiless rifle is certainly nice for its heavy power too! For early firesupport though, I still love the grand old Assault Cannon. Runt Duds/ Adventurer gear with Exploding/Superconducting rounds are terrific. I have a hard time figuring out when to move to the Grenade Launcher. At some point, forested maps become such a hassle for me that I move from indirect fire weapons to almost exclusively direct fire weapons. The GL suffers because of this. I do like that its rounds upgrade, but I often don't employ them. The same for the Auto Grenade Launcher. I think I've been put off by the weight or something, but I never do use these.
Squad Auto Fire Support Weapons
The early Boarding gun is very solid per all the earlier discussion. The custom shooty gun is amazing, as is the Super Shooty gun for the walls of lead and shear mayhem it can deliver. Auto-guns, and Machine guns, Spit fires etc, just feel under powered. Even the Gyro-stabilized auto gun feels like a waste of tech because the hitting power of the slugs are is just too light.
Under used:
LACC, Auto Cannon, Light Cannon: they never seem to make a big impression on my so I tend to pass on equipping them.
Never Tried:
Mining Laser & Rail Driver: has anyone found these useful?
Also worth mentioning:
Fusion Torch! My breaching tool of choice for Cruiser Engine Nacelles! Perfect for this.
