Invest in a good set of vinyl or paper folders, with tabs on each one. This helps get the applications into neat packets.
Separate applications by region. If you're really diversifying, looking at schools from the West Coast to the East, you can keep track of which is which by organizing your folders into categories by region.
Prioritize your top picks. Pick out the folders of the three or four schools you're most interested in and put them in a priority category so you know where they are at all times in case you need to look over details later.
Keep track of applications by status. For example, if you get rejected by a school, don't get discouraged. Just separate that folder into a box or bin where you won't get it confused with others. Then focus on your remaining folders, and apply elsewhere if necessary.
Make copies of college application essays and other documents you may want to review. When you send out an application, make sure you aren't sending the only copy of a particular document, unless you're OK with not having a paper record.
Make notes on the portfolios or other items you send to schools. If you've sent out something you haven't copied, you won't have a record. You can also track your portfolios with notes in the margin of your application folder.