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: 
Unless I'm missing something here, you mean the conference proceedings were published in the *conference series* of some journal. If this is the case, what is published is certainly peer-reviewed, but is certainly not a journal publication. A classic example in my field (Physics) is the [*Journal of Physics G: Nuclear and Particle Physics*](http://iopscience.iop.org/0954-3899). But there is a clear line of demarcation here - whenever the proceedings of any conference get published with J. Phys., they are in the [*Journal of Physics :Conference Proceedings*](http://iopscience.iop.org/1742-6596/). This leaves no ambiguity - what is published in the latter in certainly a conference proceeding and can't be classified as a journal article. (Actually, articles in the latter carry that identifier. e.g. have a look at [this one](http://iopscience.iop.org/1742-6596/531/1/012001).) 

I appreciate your concern - the only precaution that one has to take here is, not to mention an article in a manner that gives a wrong impression. This is because the rigor of reviewing process is different for a journal article and a conference proceeding (in general). For example, if the same article gets loosely mentioned as a ''Journal of Physics article'', it is inappropriate because it gives the impression that it is a journal article. That's why people divide generally divide into categories - journal articles, conference proceedings, conference talks, ''poster presented and abstract published'' sort of a thing. 

But of course, if you clearly mention/ the same gets clearly mentioned via some identifier that the article in question is a conference article, there is no harm in putting it under the heading of peer-reviewed articles. It certainly *is* peer-reviewed. 

Hope that helps.
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?