"Universal Metadata" tagging for various file types
Solution 1:
Extensible Metadata Platform, an initiative by Adobe, abbreviated as XMP.
XMP standardizes a metadata format based on XML and RDF. The data can be serialized into the actual files such as PDFs, JPEG images, MP3s, MP4s, etc.. Those file types that don't support native embedding can be annotated by just creating an .xmp file with the same name.
The Wikipedia article lists a number of tools that provide read and write support for XMP, for all major platforms.