It varies a bit from project to project, but I usually start with a custom PHP MVC framework: GluePHP for routing, Savant3 for templates, and PHP-ActiveRecord as an ORM. I'm definitely someone who prefers to work with small, understandable modules with very limited scopes/responsibilities.

I've recently considered polishing up the most-used bits and packaging it as a proper framework, but I probably need a kick in the ass (or even just a hint of interest) to do so. :)

Artpacks.org strays from the framework a bit by using Backbone.js for the front-end. So does the game that I'm working on.