All pages in root or sub-directories?
 

Definitley use subdirectories.

One advantage to using directories is that you can use keywords for directory names. Another one is that I run different scripts on different parts of sites and one script may be able to keep from generating pages with identical file names if it's the only one generating files, but if you have several scripts all making pages in the same folder you could cause quite a mess.

I prefer my folder names contain some keyterm I'm optimizing for. So if someone's looking for fat, smelly, deep-fryed widgets, they might find them at www.domain.com/fat/smelly/deep-fried/