Another alternative to Pathogen is Vundle (<a href="https://github.com/gmarik/vundle" rel="nofollow">https://github.com/gmarik/vundle</a>). I've been using this one for a while and really enjoy it.
I've been trying to replicate the filetype specific bundles using pathogen's disabled bundle feature, so unbundle is a nice discovery. To allow for more flexibility such as enabling a bundle for more than one filetype but not all (e.g. just jvm languages), there can be a separate directory that contains all bundles, and these can be symlinked from ftbundle and bundle. This also allows disabling bundles that you're still testing.
There's an awesome ruby gem called vimpack (<a href="http://github.com/bramswenson/vimpack" rel="nofollow">http://github.com/bramswenson/vimpack</a>) that makes it easy to install any VimL plugins from github directly, a la `vimpack install git@github.com:user/neat_vim_plugin.git` It uses pathogen on the backside to load the plugins. It also provides easily cloning your repo for use elsewhere. It's how I manage my vim configuration amongs multiple different computers / other developers can use my repo as a starting point. I <3.