The example PDF files aren't easily generated with TeX, so I make them in Illustrator and store them with Git. They change a little less frequently than the text itself, and usually once an example is done it doesn't get updated very frequently. In my case, at least, I can't easily version the "raw source" for the examples, as the Illustrator binary files are ~3x larger than the resulting PDFs.
I suppose I could use something like git-annex, but every time I've tried I haven't really been able to get the hang of it, and the time I'd spend learning it is better spent actually writing the thing.
(Incidentally, this new Github feature makes it much easier to browse my examples repo!)
In cases where you have to include a PDF, it's very helpful to have it be viewable inline on a page.
Also I view PDFs as only "half binary". It's just a bunch of text streams, some of which may be compressed with deflate. (Granted, there's also stuff like embedded images, fonts, etc.)