It seems that in order to force users to refresh cached static files (e.g., .css, .js) some sites (e.g., stackoverflow.com) append querystrings to the end of files. For example:
<link rel="stylesheet" type="text/css" href="http://sstatic.net/stackoverflow/all.css?v=9ea1a272f146">
I think this is a good idea, and am inclined to start doing this as well. However, I have heard that there are downsides, such as proxies not properly caching files if a querystring is present.
What are the downsides to this type of versioning?
Only one downside that I know of: proxy caching (as you said):
http://www.stevesouders.com/blog/2008/08/23/revving-filenames-dont-use-querystring/
http://paulirish.com/2010/announcing-html5-boilerplate/#comment-34976
(I found out about these from the comments in http://www.html5boilerplate.com)
The percentage of users affected by this should be very low, though. I've used this technique for quite a while, and still do.
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