Really? Most of the standard web dev stuff (Ruby, PHP, Apache, etc.) comes out of the box and works quite well, and if you need either specialized versions of things (rvm, virtualenv, custom Apache, etc.) or stuff that doesn't come with OS X (lighttpd, node.js, etc.) wouldn't it be installed in /usr/local?

I don't think this will break many web dev tools. Unless you mean stuff like Sequel Pro or TextMate; even then, I can't imagine most apps won't make the transition smoothly.