Ok... I'm going to tell you how to set up rebase to ALWAYS rebase on ALL repos. If you don't want this for all repos, then you can do this on a per-repo basis by doing all the config without "--system". Also, you can use "--global" instead of "--system" if you want to ensure that other people that use your machine aren't affected by the setting (nobody else uses my machines, so I don't care and do all my config at the --system level).
So, to set up all "master" branches to do rebase by default - do the following:
git config --system branch.master.rebase true
To set up all "new" remote tracking branches to be created with rebase by default, do:
git config --system branch.autosetuprebase always
If you already have remote tracking branches, then I recommend you make sure you're current, delete the local branches, and recreate them (1.7.x does this automatically if you use the branch name to check out the remote branch, so make sure you're using Git 1.7.x or later for that hawtness (as darkxanthos would say)).