Should a conference paper in a journal be considered a journal article? I have recently been doing a revision in my CV. I organized my publications into "Peer-reviewed journal articles", "Peer-reviewed conference papers", "Other published papers" ...

My dilema is which section to choose for conference papers published in a journal (either regular or special issue). Which of these two criteria should be used for classification of publications: the paper origin or the publication type?

Assumed, I have chosen journal article section for some of my conference papers. Could omitting conference details be treated as misleading?
To the best of my understanding, the key reason why some conferences publish their proceedings as journal special issues is precisely to enable the papers to be listed as journal papers rather than conference papers.  This is essentially a kludge to get around bureaucrats and people from fields with an "only journals count" prejudice.  

As such, I think that it's entirely reasonable to list such papers in either the conference section or the journal section.  The "technically-a-journal" form, however, typically has different citation information than the conference publication, so if you choose to list them in the journal section, be certain to list them with this alternate citation information, as reported by the journal archive site.