Question: In a "list of publications" (e.g. for a PhD thesis), should a conference paper which is published as "proceedings" in a peer-reviewed journal be categorized as a "journal article"?

(I'm from Liquid Crystals field.)

Answer: 
As counter-intuitive as it sounds, there is no absolute rule for what is considered a "journal" and what is considered "conference proceedings". In most cases the distinction is trivial. Most journals are not associated with a specific event, and paper submission and review are entirely unrelated from any conference or meeting. Contrary, most events have dedicated proceedings, which contain all and only the accompanying papers to the presented talks. 

However, there are curious cases where the line blurs. Some conference proceedings have self-styled themselves as "journals", presumably in an attempt to make their publications seem more important. A slightly different case is [VLDB](http://www.vldb.org), which basically does not do actual peer-review of conference submissions anymore. Instead, you submit to the VLDB journal, your submission gets the traditional journal peer-review process, and once a year the authors of all papers accepted in this year for the journal are invited to present their paper at the annual meeting.

This is all to say that I think the "clear line of demarcation" isn't quite as clear as New\_new\_newbie says.

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> In a "list of publications" (e.g. for a PhD thesis), should a conference paper which is published as "proceedings" in a peer-reviewed journal be categorized as a "journal article"?
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If it is called "proceedings", I would put it to the other conference papers. However, to be on the safe side, you can always just check how other authors of this conference are referring to their paper. Are they treating it as a conference talk, or a journal submission?
As long as you don't say anything that is not true, and do not go against your university's regulations, you can use the layout that you like the best.

In my thesis I categorized publications into:

* Peer-reviewed articles
* Conference talks
* Conference posters

In "Peer-reviewed articles" I included any papers, including proceedings, that had been peer reviewed (i.e. I received an anonymous referee report for them). Anyone interested in reading my thesis will be familiar enough with the journals to know which ones are a conference proceedings venue. Certainly my thesis examiners were.