Academic papers, patents, textbooks, anything with citations also works
In order to rank papers I think you would instead have to rank people, so that the people who have written on Paper X can in Paper Z reference the authors of Paper Y.
But of course it would need a CiteRank of equivalent quality to pagerank to be at all useful.
A paper X has been updated to reference a response or later work Y, which itself referenced X from the start in such a way as to make the 'version' of X in the reference unknown. Citation-trawling software might bite hard on a loop like that :P
Anyway, I also wonder why having cycles makes PageRank useful and lacking them makes it less so -- you can still count inbound links and such with a DAG, and huge huge amounts of the content of the web would exist in DAG-equivalent subtrees, wouldn't they? I could have this pretty wrong, haven't looked at the paper in years and should go do so!