I have 2 blogs, one hosted under my main domain, and one on a subdomain. I would like them both to use the same hostname for CDN served content (static.joostschuur.com). For media library content, this seems to work just fine. I set my Settings -> Media -> 'Full URL path to files' to http://static.joostschuur.com/blog/ and http://static.joostschuur.com/idg/ respectively, and by some behind the scenes magic, it looks like you subtracted the hostname that I provided in my CloudFront settings from the URLs above and figured out that you needed to place files in a sub-directory. Quite impressive, I was actually looking for an option to configure that, and didn't expect this much magic.
However, when I exported my theme data, it proceeded to add that to the root directory of my CDN bucket, i.e. static.joostschuur.com/wp-content. This means 2 sites couldn't share the same hostname. Have I hit a scenario that W3 Total Cache can't handle right now?
I tried appending my subdirectory to the bucket name or hostname under my CDN settings, but both broke the CDN test.
I'm currently running 0.9.1.1.