This list of mods is built around the excellent Ghost Mode overhaul mod. All of these mods are compatible with it.
If I had to pick just 3 mods to use, they would be Ghost Mode, Friendly HUD, and Enhanced Targeting. All three enhance the game significantly while leaving the vanilla feel in place.
Most of the other mods are for convenience or improvements in the user experience. Auto Apply Oils is the one mod in the list that does away with a core game mechanic. It even renders the 3rd-level alchemy skill Fixative useless, so decide for yourself if makes the game too easy before using it.
There are no texture/lighting/weather mods in this list since I personally find the base game has very good art direction and has a consistent look