Comment Pseudo code it. (Score 1) 254
Pseudo code it.
Read the major blocks of the application in what ever editor makes you happy, with a text editor next to it ( preferably one that does arbitrary text folding ) and just psuedo code the hell out of it. The more of this you do, the more you'll be able to look back at your own pseudocode for a definition of some obscure thing, and the more a pattern will appear as you notice yourself typing the same things over and over again.
Also works as sl/hack documentation when you're done.