This requirement has arisen from the issues we face with performance and looking at any Sitefinity site you can very quickly see one of the major problems which is too many connections. (Asp.net webforms pays a big part here), but we're looking for a more permanent solution in Sitefinity.
So in terms of which files? As many as possible without affecting the rendering and functioning of the site.
I've noticed that Sitefinity does indeed use the version query string, but what we've also noticed is that for some unknown reason, when we deploy new stylesheets to our production server and send out a link for management review, many times they don't see the changes. The only reliable way to have the changes show up seems to be restarting IIS or the application pool, which in a production environment is not a good answer. We're unsure of exactly how and when the versioning number is updated. And, if output caching is in use, we're not sure if Sitefinity is caching the reference to the stylesheet as well, which would render the version query string somewhat useless, or rather, dependent on the output cache changing.
At the end of the day we're just looking to standardize our Sitefinity implementation in such a way that it becomes easy for our developers to leverage a pre-built tool or method that will allow us to produce sites that massively reduce the number of HTTP connections, however that must happen.