I've downloaded far too many apps -- over 400 at this point. I organize them by function such as Office Apps for Quick Office, DocsToGo, and the Apple Suite. I have a folder for remote access to work and home computers, another for browsers, one for utilities, reading apps, music apps, video apps, etc. For Games, I have a bunch, so I needed to break that down further -- like arcade games, puzzle games, adventure games, etc. Just play around with it and you'll find your groove in no time.
