It depends on the type of app. If it's a rails app, I usually start with user.rb or whatever the equivalent is (account.rb or something) as those usually have most of the functionality. From there, I'll either look start looking at routes config and going from there or some of the base controllers to get a sense of things (i.e. ApplicationController or maybe AuthenticatedController).

For non-rails web apps (and rails apps), I'll usually find a portion of the UI and just start tracking from the front-end to the back-end. Something like finding some text on the page, and trying to reverse back to where that particular piece of text was defined and what steps it took to get there (which view, helper, controller, etc.)

For non web-apps, I don't have any good techniques, unfortunately.