My preference has been to write directly on the bone with an archival India ink. In my opinion, the catalog number should be irreversible. However, I have been told that I am a dinosaur for this preference, the technique should be reversible. I still write directly on the non-showcase specimens.
In my experience, the acrylic base coating method is undesirable, and I much prefer the Japanese paper technique. At some point all or part of the acrylic chips or peels off and one is left with a partial number. It can also be difficult to write clearly and not smudge on the acrylic base, or run when the clear overcoat is applied. Japanese paper will not chip, and should not peel off under normal handling, and it conforms wonderfully to the surface of the bone in a way other paper will not. So, unless I have an absolutely black bone, I do not use a white acrylic base coat – even then, I prefer to use acrylic white for numbering followed by a top-coat. And the more I think about it, the more I abhor the acrylic method – it peels and chips!
My personal preference in pens is the Faber-Castell Pitt artist pen. These pens have demonstrated superior light-fastness and they tend to out-perform the Microns and others in just about every way. [Amy Davidson and Marilyn Fox have a paper on this subject in a March 2011 SPNHC newsletter.] I also prefer a top coat with any of the techniques to keep the smudge-factor low.
Amy Davidson and Marilyn Fox also have a run-down of various techniques in a poster – which is up on Amy’s Academia.edu page.