Arkhein posted about an interesting book that goes into how geography shapes history. Well, that history then leaves traces of itself on the geography in the form of names.
This probably isn't new to you if you've been interested in making your own worlds, but I thought these were a couple cool examples of the linguistic evidence historic events leave on a landscape.
Here you can see the various names used for waterways as evidence of the different languages used by the colonizing cultures.
in the U.K.
So, once you figure out your geography, then figure out how that shaped historical events, then figure out what languages your various cultures used, you can name places based on that information. Piece of cake!