I love pathogen for managing my vim plugins. It allows me to put plugins in my ~/.vim/bundle directory and have the confidence of being able to simply uninstall them by deleting the plugin directory. Since nowadays almost every vim plugin has a github repository, it's very simple to do a
git clone <paste> in the ~/.vim/bundle and then later update it with a
git pull. Since a
git pull will do nothing to a directory that either isn't a repository or has changes, you can safely execute it on all the directories in your bundle without worrying. I made a simple command to put in my .vimrc that will do just that.
command! -nargs=0 Update :!find ~/.vim/bundle -type d -d 1 |\ while read line; do\ echo `basename "$line"`;\ cd "$line" && git pull; cd -;\ done