OCR software like ABBY can spit out something called a "searchable PDF", which has a text layer underneath a picture of a scan.
Otherwise, PDF has 'dictionaries' with arbitrary key-value pairs in them. The "Info" dictionary has some specific metadata fields like Author, and a "Font" dictionary embeds fonts, but you're free to use those dictionaries for whatever. There's also a standard to embed 'dublin core', rights management and custom metadata called XMP. Files can be embedded. You can also use comments, as PDF is a subset of postscript.
When a PDF gets converted to PDF/A (by archiving software) or flattened/optimized, most of these are likely to be lost.
