For WAV, AIFF, PNG and other IFF-like file formats, there is a standard way: define additional chunk types for your additional metadata.
For the other file formats in question, you can use format-specific extensions as you summarized.
In HTML that could be
<meta> tags, or
<!-- comment --> tags containing structured text, or custom
attribute=value pairs. If the custom metadata is binary, you can encode it with base64 to include it in HTML.
All these format-specific extensions will require custom reader/writer code.
Alternatively, you could store the additional metadata in a uniform way outside the files. That could be in a database, a sidecar file per data file, a metadata file per directory, or other place.
If the data files are all inside a zip file, you can use zip comment fields.
If the files are all on Unix (including macOS) and Linux, you can use extended file attributes (xattr).
Some file systems support a "file system fork" for each file. On Windows NTFS it's called an "alternate data streams (ADS)".
The design choices have the obvious tradeoffs in which operations preserve or drop the custom metadata.