Actually, what I found sorely missing in php and started loving in the ruby world is bundler. It's not a package manager, but a dependency manager. You feed it a list of gems that you directly depend on and it figures out which gems to install in which versions so that all direct and indirect dependencies are satisfied. If it can't, it prints a meaningful error message. On top of that you can stack tools like gemnasium which track which of your dependencies were updated.
I do have a couple of projects that depend on about a hundred different gems. Managing that would be impossible without bundler. On the other hand, having a tool that enables you to manage this complexity makes you write smaller and smaller self-contained, separately testable gems that just add some little piece of functionality on top of some other lib or pulls together multiple libs and adds the glue code. It's actually common that even full-stack frameworks like rails or padrino consist of a handfull of separate pieces with another gem gluing them together. Even ORMs such as datamapper come in pieces.
I know of no tool in the php world that even attempts to solve this problem.