The current stable version, and the version shipped with TeX Live 2012, of the microtype package is 2.4. It is not compatible with XeLaTeX. To get it working with XeLaTeX toy need the latest beta version (as of writing version 2.5 (beta-08)). It is possible to obtain it from tlcontrib.
After downloading the package and extracting it (tar xvf microtype.tar.xz) you need copy it to your TeX Live installation.
Instead of overwriting the current package in texlive/2012/texmf-dist/ it is better to place it in its proper place at texlive/texmf-local/. That way when you update TeX Live it will not be overwritten.
After copying the package you need to run texhash to make TeX Live aware of it.
Now you should have microtype working with XeLaTeX.
This should also work with older versions of TeX Live, but I have not tested it.
I did SSH into my server running Ubuntu 10.10 from my laptop running Arch Linux with a rxvt-unicode terminal and received the following error when I tried to run screen: Cannot find terminfo entry for 'rxvt-unicode-256color'. or when i tried to do a clear: 'rxvt-unicode-256color': unknown terminal type.
To add the terminfo entry you can take the the terminfo from rxvt-unicode and add it to a file:
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