General Overhaul: Qarl's Texture Pack 3 (alternatively QTP3 Redimized / Reduced / Redimized and Reduced if your PC can't handle the full QTP3; Redimized runs smoother and doesn't sacrifice much visual quality) and Bomret's Texture Pack (this covers SI)
Caves: Ampol's Cavern Retexture
Flora: Enhanced Vegetation + Improved Trees and Flora + Improved Trees and Flora 2 + Better Nirnroot
Miscellaneous: Better Staffs Texture + Improved Fruits, Vegetables, and Meats + Kafei's Better Amulet/Ring Replacers + VA's Better Gold + Book Jackets (Oblivion and KotN)
If you want your water to look better, install OBGE and OBGE Liquid Water.
The best weather mod, IMO, is All Natural. You can also install Natural Environments, but only enable the Natural Habitats component of it (Vegetation, Weather, and Water are already covered).
For better and more immersive sound: Better Bell Sounds + OSSO + Sounds of Cyrodiil + Symphony of Violence + Storms and Sound