Just though of another one! This worked surprisingly well and was really annoying at the same time.

The huge application consisted of a single PHP file. If you guessed that it was tens of thousands of lines long, you'd be wrong. It was only a few hundred lines, if not less!

The trick was storing code in the freaking database. The mother of all index.php's would simply query for the correct piece of code based on query parameters and eval it! They had an editor where you could make live code changes to the page, and even some rudimentary version control. Amazing times!