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 -;\