http://www.nitro-it.com.au/downloads/link.zip
This script adds rel meta to <a> tags in CKeditor. This is especially handy if your project includes lightbox! (the reason I added it)
Just overwrite ckeditor\plugins\link\dialogs\links.js for all the rel goodness!
You can find it in the advance tab of the link popup.
Note: you may have to refresh the cache for it to show up.