Biggest sin: I had a short term contract which I discovered half-way through was indirectly for the Pentagon. I didn't quit.

Biggest challenge: I am in a contract where we have a setup not unlike what you describe with the PHP. We're using home-rolled templating to dovetail into TT2, in three different ways, and every reasonable base package that we use is wrapped in home-rolled versions which do not inherit from the base packages, truly just wrap them, while often inheriting from other internal packages which are manifold... and in some places rely on similarly redundant and wrapper-based PHP, and that' really just the beginning. It's almost the best part about the setup. I really like the people (they know the problems and are trying to dig out from the spaghetti) and the money is excellent but now and then the "challenges" feel more like a Hemlock Society recruitment seminar.