Q:

How many arXiv papers are uploaded in their final (refereed) versions? 

In a recent meta.physics.se discussion on the use of permanent links form physics.stackexchange, I proposed as policy that

when linking to the arXiv, link to the abstract page (arxiv.org/abs/...) and not directly to the pdf, as a courtesy to users on lower bandwidths.  If the paper has been published (which will be noted on the arXiv abstract), include a link to the journal version, even if it's paywalled, if only as a courtesy to the referees' hard work. 

One comment on the italicized part was

Doesn't pretty much everybody post the final version on arxiv? 

and I would like to know (if that is even possible) to what extent this is true.  My gut feeling is that this is field-dependent, but I do not know what evidence may be available to explore this, other than anecdotal evidence. 
Thus: Is there a clear trend for authors to upload post-referee-process versions after publication?  Does this depend on the specific field?  What evidence is available for this? 

A:

It is a lot of work to find out which paper in arXiv has actually the same content as a published paper.  However, taking arXiv's journal-ref field as a surrogate indicating which paper has a journal version out, I arrive at these fraction of papers: 

So it looks as if the gut feeling that this is field-dependent is true: high energy and nuclear physics have consistently high fractions of papers with journal-ref field set.  On the other hand, this seems far less common for maths papers.   Note that a certain drop at the end is to be expected as the preprints may be uploaded to arXiv considerably before the paper is accepted, printed and the journal-ref is updated in arXiv.  
Here's the marginal plot over all fields:
 
So overall, about 45% of the papers have a journal-ref.  However, it is set for almost 60% of the 2001 - 2007 papers.  Whether this is a real decline or just the lag between preprint and paper publishing remains to be seen (in a few years). 
Also, neither the overall nor the subject-dependent trends seem to have a convincing increasing trend, even if the decline due to "not yet published and updated" is assumed to be the sole cause of the decreases.  
For the complete picture, here's the development of total number of papers:

and number of papers with journal-ref set:

