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.
Please don't password protect PDFs for books. It makes it a huge pain in the ass to actually read. I'd much rather you do what the Pragmatic Bookshelf does and just embed our name into the PDF.
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.