advice on biuling large apps

Hi, Over the past few years I've put together my own code base and coding style which enables me to build sites, and drag'n'drop features and add-ons into simular projects without any grief. But I'd like to push it one step further... I've got a few ideas about where I might head, and have seen some stuff on google, but I thought I'd ask here as well, to see if anyone can recommend any articles I might want to look at. In particular, I'm interested in how I might separate modules or plug-ins into folders, rather than my current flat hierarchy (everything in one or two include folders). End of the day, I'm aware that I'll need to spend a bit of time playing with code to come up with what I want, but there's no harm in hearing what others get upto :) Cheers, Justin