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 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.