Tracking updates for an individual paper in arXiv
This is a pretty silly solution, but you can use a page tracking service to see when the page changes; this should detect both changes in the paper as well as in the journal its submitted to.

Edited as per Jaap Eldering's suggestions in the comments: you can use arXiv's OAI-PMH protocol to programmatically access version history! For example, if you want to look up arXiv #1206.0094, you can look up http://export.arxiv.org/oai2?verb=GetRecord&amp;identifier=oai:arXiv.org:1206.0094&amp;metadataPrefix=arXivRaw for its version history.

Furthermore, arXiv does have an Atom feed for individual articles: you can access it at http://export.arxiv.org/api/query?id_list=1206.0094 -- the link it includes is to the latest version of the article, so I presume it will change if the article is updated.