Lulu? At least that's the only place I've specifically bought a PDF - then I found out that it's wrapped in some horrible Adobe DRM (if there are any ways to remove this, I'd love to know). I don't begrudge the money, I just wish I could read it in Preview.app rather than Adobe Digital Reader or what ever it's called - it doesn't scroll smoothly, only page wise which is a massive pain when there's lots of diagrams.
Other than that, all the ebooks I've bought from individual storefronts, often from having seen them on HN, have come as a PDF/epub/mobi bundle to work on any device.