Fabricskyboxes directory: assets\fabricskyboxes\sky (.json files)
Optifine directory (pre-1.13): assets\minecraft\mcpatcher (.properties files)
Optifine directory (post-1.13): assets\minecraft\optifine (.properties files)

BE SURE YOU DELETE THE .JSON / .PROPERTIES FILES, NOT JUST THE TEXTURES!

Blood Moon: 		requires too much reconfiguration to be removed
Blue Moon: 		requires too much reconfiguration to be removed
Lightning strikes: 	delete sky 303-314, 324 and 325
Supercell: 		delete sky 200 and 300
Rainbow: 		delete sky 260
Seasonal Sun rotation:	requires too much reconfiguration to be removed
Noctilucent clouds:	delete sky 328 and 329
Asperitas clouds:	delete sky 322 and 323
Mammatus clouds:	delete sky 318 and 319
Fiery sunsets:		delete sky 326 and 327
Tornadoes:		delete sky 315-317
Solar eclipse:		delete folder "401-500_solar_eclipse"
Gas giants:		delete sky 103-106
Auroras:		delete sky 301 and 302
Shooting stars:		delete sky 119-122
Meteor shower:		delete sky 123-125
Black hole:		delete sky 101 and 102
Light pollution:	requires too much reconfiguration to be removed
Outer space:		delete sky 500-600
Hurricane:		delete sky 320, 321 and 503
End skies:		delete folder "end" / "world1"

Other features like weather clouds or high altitude clouds are not listed, since I see no point in removing them.