It is always good to follow best practice when it comes to HTML specifications and suggestions.
12.3.3 Links and search engines
^ Check the examples.
I use link rel quite frequently. And no, I don't know what impact it has on the search engines. I do know that certain things seem to happen that I cannot fully explain like the persistent return of indented results where link rel is being utilized. Again, I cannot confirm that it is the link rel that causes the indented result. If you think about it though, if you are using link rel to group documents together, wouldn't you think that would be a cause for indented listings? ;)