I agree that versioning the resource representation better follows the REST approach...but, one big problem with custom MIME types (or MIME types that append a version parameter) is the poor support to write to Accept and Content-Type headers in HTML and JavaScript.
For example, it is not possible IMO to POST with the following headers in HTML5 forms, in order to create a resource:
Accept: application/vnd.company.myapp-v3+json
Content-Type: application/vnd.company.myapp-v3+json
This is because the HTML5 enctype attribute is an enumeration, therefore anything other than the usual application/x-www-formurlencoded, multipart/form-data and text/plain are invalid.
...nor am I sure it is supported across all browsers in HTML4 (which has a more lax encytpe attribute, but would be a browser implementation issue as to whether the MIME type was forwarded)
Because of this I now feel the most appropriate way to version is via the URI, but I accept that it is not the 'correct' way.
