I've noticed a couple of issues with:
Bloodmoon Overhaul + Frostmoth Docks Expanded (clipping issues)
Frostmoth Docks Expanded + Ships of the Imperial Navy - Bloodmoon version (clipping issues)
Neither of these issues should cause a crash, but visually they look a bit off. I've also noticed a variable level of problems with anything that alters the landscape and the popular grass/groundcover mods - you can often find floating or half buried groundcover as a result. Whether it's really noticable or not is another matter.
Atmospheric Sound Effects + Realistic Weather -> both of these alter Regional settings, so they conflict. The last to load should take precedence (or you can copy the adjusted weather percentages from RW into ASE and disable RW).
More Detailed Places Compilation + Mournhold, The Great Bazaar -> I noticed that several of the 'teleport' doors introduced to towns like Ebonheart etc were blocked by crates/barrels.