There are console commands such as
SetDelete and
Disable you can use but I'm unsure if they would affect save game stability negatively so I hesitate to recommend them. Perhaps someone else can chime in to say for sure if they are safe to use for what you want to do with them. Reference for these commands is here if you feel like trying it out: http://www.uesp.net/wiki/Tes3Mod:SetDelete
If you're using a mod that adds random merchants such as
Morrowind Comes Alive or
Starfires NPC Additions you can do as I do and just sell off any items you think are overpowered or useless for 1 gold and the next time that cell or NPC cycles it's effectively gone as a new random NPC with a completely new random inventory will spawn in the original place.