They are not usually listed on the same list as “regular papers” in a CV. The reason for that is that they are not peer-reviewed. In the fields of physics, chemistry and biology, it is most common to list your scientific production in a CV by breaking it down into the following categories:
- Peer-reviewed articles
- Book chapters
- Conference proceedings
- Invited conference talks
- Conference talks
- Conference posters
I looked at examples from the Biophysical journal supplements, and the abstracts are quite short (one paragraph or two). Even though it is published in print, it is too short to be considered proceedings. Thus, I would list it as either a talk or a poster. That is was published as part of a supplement to one journal does not make it very different from any other conference.
In some countries and in some fields, it may also be typical to further break down between national and international venues (journals, conferences, etc.).
As a side note, the journal webpage has some information on how to format such citations:
Smith, R., S.E. Jones, T.J. Smith, (2006) Histone phosphorylation in DNA damage. 2006 Biophysical Society Meeting Abstracts. Biophysical Journal, Supplement, Abstract.