Darkness usually means that the PCs have forgotten to bring torches and/or light spells, that they are all elves/dwarves/half-fiends/etc. or that they're sneaking up on somebody.
Seriously, though, I use about as much darkness as light in my games - and it usually means night.
Kinda figures, too, given that many of the people my players' characters usually interact with (as well as quite some of the PCs themselves) are of a shady nature (e.g., criminals, monsters...).
Rain, fog and mist are common as well.