as for my self running many mods i have only had 5 problems 3 of them were conflicts with mods so i could fix them myself so ill start the forum of with 2
1: The well reported on glitch with breeze home upgrade of alchemy lab
2: The obvious faction problems where Dawnguards and Vampires will for some reason find u as enemy and attack breaking story missions (I have only had problem with Vampire side on two characters the 1st was at the point when u have kill serena's farther as when i entered castle all vamps attacked me as soon as i entered and they are almost all unkillable XD, the 2nd was on my other character entering the vamp castle for the 1st time on her with serena *i was stage 2 vampire already through normal means* and again everyone inside attacked me) i should mention aswell that i had no crimegold and it wasnt me factions either as i set them all to 0 using Console comands trying to fix problem also i was not in armor that increases threat.