Stun batons work great for me.
I used cattle prods at first, but but never loved them because slow and unwieldy. At some point I noticed the baton's damage bonus, checked my gal's stats, and gave it a try. I get three dings out of them in the time it takes to prod someone once -- this certainly helped. Next thing I noticed was that it trains not only melee, but reactions as well. Suddenly all my gals had 100+ reactions.
It's a "don't leave home without it" item and I successfully use it on everyone not wearing power armor: academy medics and engineers, guild engineers, church priests and matrons. Even lobstermen! It's one-handed and small and often good enough. By the time I could have a lasso ready, the baton has already done the job and is back in the holster.
However, lately I run into opponents where the baton is no longer enough. I had high hopes for the poisoned dagger: "Stun damage modifier: 100%" it says. I thought it would do a lot of stun on top of the HP damage, but that doesn't seem to be what's happening. I had my second encounter with MERCs the other day and it typically took some 3-5 stabs of the poisoned dagger to put them down. Most of the time, the final blow was also fatal. So I guess the poisoned dagger is much less stunning than I thought it would be. Looking around for alternatives, I don't see any. What to do?
I share my experience: The Stun Baton is amazing for everything until medium armor. I have some lassos around for flying enemys and high armor (Still useless against exosuits).
I like to use the Tazogun for non-lethal infiltration mission, because of the reaction snapshot.
Poison in general is a gamble. It has like a 50% chance, depending on the enemy and weapon, to kill instead of stunning. I also use a Spiked Mace to stun exosuit units in early-mid game with more deaths than stuns.
Don't try to stun every MERC or similar unit, unless you have late game weapons like Neural Whip. Just kill them and make them surrender. Don't risk your units needlessly.