KO grenades are pretty good against enemies with 400% choke resistance. Which is a lot of them. EMP grenades can work well in certain situations since they have a lot of armour reduction. There are quite a few aliens who are part machine.
TGL blunt rounds are my preference for non-end-game gear, unless you're against something fragile. Gas and chem weapons have a somewhat passable chance to stun, but are even more dangerous.
Small Launchers are still pretty good if not the end-all-be-all of stun weapons any more. The Hadriex Gun is somewhat similar. Armour-piercing, but less power and you need ghost juice and a psyker to power it.
Neural Whips are an interesting alternative to Power Maces, ignoring armour instead of stripping it. Rare and probably less useful overall, though. Of course, the problem with all melee weapons is that you have to get close to the enemy, preferably around them to their back as well, and then - probably after a lot of running - still have energy left over to kill them and take cover. Which tends to work about once before needing a rest or some stims. Oh, and hope their dodge value doesn't make it a crapshoot.
There are also the dart guns, which are pretty useless as they are. They should have their listed damage values halved to not mislead the player. I've removed the double random rolls and given them 25-75% armour penetration depending on toxin type, and now they do pretty nicely as long-range stunners. Still need to dart tougher enemies a few times, but across half the map it's not too bad.