I've been working recently on a package manager for PHP 5.3.1, inspired by rubygems, bundler and npm.
I'm doing my usual thing of README-driven development so there is a lot more described in there than actually exists.
Basically Phark manages packages either globally, or installed per-project in a vendor directory. It hooks into projects via an auto_prepend_file hook and sets the include_path on each request. I don't particularly love this bit, but short of an extension I can't see any other elegant way to do it.
I'd love feedback, criticisms, suggestions, etc.