The rage these days seems to be to keep your own dotfiles repo, complete with some kind of install mechanism.
My own is here [1] but it covers my whole homedir, not just VIM. I use Rake tasks (originally inspired by @holman, I believe) for install / update / clean.
There is a bootstrapping problem when using Vundle with many plugins [2]. The only way to have your Vundles install cleanly the first time is to split up .vimrc into two separate files, which is what I have done.
https://github.com/gmarik/vundle
You just copy your .vimrc over and Vundle installs everything.