I have never heard about an application for this speciality. You asked two or three questions: One about html files: well, any html editor can do that, and another question about universal or at least "some" file types - I guess you mean text-based files: WordPad or any other Rich Text editor. But they might change the original format. If the file is not a text file, you can use almost any screen capturer's picture editor, but obviously only on a picture copy of the original "thing".
Yeah Curt. Perhaps I am asking a some sort of internal database (or even a database in the cloud like some addons prepared to mark the web and share those marks)
I remember a trial : Xentient Labels http://xentient.com/http://xentient-labels.softonic.com/
but seems a project abandoned.
I think that project put the marks independly of the file. Only for mark file names in explorer. A sort of database control I suppose.
When you mark a book or a file you personalize.
In the case of the book is relatively easy delete the mark if were made with a pencil....
In the case of a file is simple made a copy of the original.....
Perhaps you want to have the ability to decide read/send with marks or not.
Or mark directly a simple txt file. Obviously that txt file will not be read with marks from other pc, unless you convert to doc or rich text.