Meteor downloads all the packages in the user directory in ~/.meteor/packages. There is no command to clean up this directory, as Meteor doesn’t know the dependencies of all the applications on your computer.
As my partition is always too small, I just wrote a one-liner to solve this problem:
cd ~/.meteor/packages; for i in * ; do pushd $i > /dev/null; ls | sort -V | head -n-1 | while read v ; do rm -rf $v .$v* ; done ; popd ; done
This will delete all but the newest version of every package. If an application needs an older version, it will be downloaded and re-installed by the next start of this application.
It saved me 2.5 GB today. The script works very well in Linux, it should work on Mac OS X as well.
If you delete the link to the meteor command line tool by mistake (it happened to me in the first version of the line above, which contained a bug), you can use the following command to recreate it from the newest version available:
cd ~/.meteor/packages; ln -sf `ls -d packages/meteor-tool/* | sort -Vr | head -n1`/mt-os.linux.x86_64/meteor .
Use all the commands with caution and at your own risk.