I use pathogen for organizing my vim plugins. I git clone the plugins from github into the vimbundles directory. This way it is simple to update them.
vimbundles
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Randy's answer works best for me. A one liner I use when I want to add the ignore = untracked option to a lot of submodules is:
for s in `git submodule --quiet foreach 'echo $name'` ; do git config submodule.$s.ignore untracked ; done