"Classic" Monsters
This may go along with the whole “monster palette” discussion, but one thing I do is tie the origins of certain “classic” monsters to the world itself. Many monsters have their source in our own mythologies, but where do they come from in your own setting (whether it be homebrew or store-bought)?
For example: Medusa from Greek mythology dared to compare her beauty to that of Aphrodite and was punished. – where do Medusae come from in your world?
An example from Aquerra would be manticores, who are actually. . . wait, I can’t use that one b/c my players may see this. . . But when they faced one they were amazed that it seemed to be able to do more than what they thought a manticore could.
Ok, drow in Aquerra are not a race unto themselves, but a template applied to any evil elf that dedicates herself to the spider goddess – this only slightly changes the origin of drow –but also adds flavor in that the PCs suddenly realize any elf can be a “drow”
The origins of certain monsters will also help create a world context, and maybe even allow PCs to figure out better ways to deal with them as they gain this knowledge, w/o actually having to change the rules all that much if at all.
So ask yourself, where did pegasai come from? Or unicorns? Etc. . .