Has anyone noticed that trapping living beings souls and then using them to enhance armor and weapons seems rather immoral? *Do do do, just walking along, AH I'm dead shot buy a soul capture bow. Ach, my soul is in a gem... *10 minutes later* hey now I'm a sword! Nice! Wait, everytime the sword hits something I feel I'm losing something, ZOMG MY SOUL IS LOSING CHARGE! *30 minutes later* the soul is gone and destroyed... killed.....*
Yeah, that's why I don't use enchanting. It's sick and diabolical. What do you think

Funny because I thought of that back in Morrowind and Oblivion. I thought that while it was ok to kill monsters indiscriminately, I hesitated to use their souls because surely they deserved a better fate.
But you can set your conscience at ease. Souls from animals and monsters are fair game, because it's pretty much like killing animals for food and killing monsters to protect the world.
Although humans like bandits do deserve to die for attacking you, trapping their souls can be akin to illegal war crimes. Sure soldiers have no problem killing people in wars, but there are still war crimes like using biological weapons and illegal torture that you cannot do. In the same way, killing bandits is ok, but trapping their souls is considered an act of evil.
Lorewise, humans that trap other human souls are often evil people who have no moral values, like necromancers. I'm sure when going through their hideouts, you find a lot of evidence of murder and torture going on.
In Oblivion, the Mages Guild has outlawed necromancy. In one of the quests in Cheydinhal, you found black soul gems belonging to Falcarm which is considered necromancy.
Black soul gems = can trap human and daedra souls.
Black soul gems = necromancy.
Necromancy = evil.
Therefore, trapping human souls is evil.
http://www.uesp.net/wiki/Oblivion:Cheydinhal_Recommendation
So in conclusion, soul trapping animals and monsters like trolls are ok, but soul trapping humans is the one that is actually immoral.