I've been asking that question myself lately...
A) Some games are sure to sell out as soon as they hit shelves, pre-ordering in those cases make sure you get the game on release date.
B)Sometimes you get "extras" for pre-ordering, such as exclusive items, discount at DLC, DLC for free, and other stuff. Also justifies pre-ordering, even digital preordering.
C) Makes no sense: pre-ordering digital games (or movies or songs) when you don't get any sort of incentive for it... I'm a fan of digital purchases, movies, songs, games etc. If I can buy it digital, that's how I'll probably roll. The other day I'm at the iTunes store, and I see Django for pre-order, that's when I asked myself, there're no extras or discount for me to buy it as a pre-order, nor is iTunes going to sell out all the movies because, well, it's DIGITAL...
What I think, many people, me included, sometimes go on auto mode and don't think while pre-ordering: I pre-ordered The Dark Knight Returns - Part 1 at iTunes, that didn't cause me any problem mind you, I paid a normal value, and got my product as good as any, but there was no valid reason I couldn't wait and just buy it later on. I believe we're so used to the pre-order thing of hard copies that CAN sell out, that sometimes we no longer think about the reasons for a pre order...