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: 
Allow me to disagree with @xLeitix.

No. It's a conference paper.
----------------------------

A paper qualifies as a "journal publication" if (and only if) it passes through the standard peer-review process for the journal in which the paper is published. If a paper is reviewed only by the program committee for a conference, it's a conference paper, even if the proceedings are published in a journal.

As a particularly confusing example, consider [SIGGRAPH](http://www.siggraph.org/), the flagship conference in computer graphics. For many many years, SIGGRAPH has published its proceedings as a standard issue of the journal *ACM Transactions on Graphics* (aka "*TOG*").

SIGGRAPH accepts two types of papers: (1) direct submissions to the conference in response to the call for papers and (2) papers published in *TOG* in the last 12 months. Papers accepted from *TOG* are clearly journal publications, because they went through the standard *TOG* refereeing process. (Those papers are not republished in the proceedings issue of *TOG*, but they are listed in the "table of contents".) But direct submissions accepted by the program committee are *not* journal publications, because they did *not* go through the standard *TOG* refereeing process, even though they are published in *TOG*.

The distinction is all the more confused by the facts that in the graphics community, "SIGGRAPH paper" is a *considerably* more valuable label than "journal paper", in part because the reviewing process for SIGGRAPH is (or has been historically) considered *more* rigorous than the refereeing process for graphics journals. 

Of course, the rest of the world doesn't share this preference—or perhaps more accurately, doesn't believe that anyone sane could have such a preference—which is *precisely* why SIGGRAPH publishes their proceedings in a journal. Put bluntly, the graphics community chose to defend itself against lazy scholars who value the imprimatur of a journal above the quality and impact of the work through deception. Or if you prefer a slightly less inflammatory term: camouflage.

It's worth noting that [ACM now explicitly forbids conferences from publishing proceedings in an ACM journal](http://www.acm.org/publications/policies/conference-proceedings-in-acm-journals). (SIGGRAPH's practice is grandfathered.) But this doesn't stop non-ACM conferences like [VLDB](http://www.informatik.uni-trier.de/~LEY/db/conf/vldb/index.html) from wearing similar camouflage.
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.