Hi Matthais, I've spent a really long time looking for a good BibTeX editor on Windows and, I'm sorry to say, I haven't really found one. In my opinion, the very best BibTeX editor is BibDesk (Mac OS X only) followed by Pybiolographer (Linux only). JabRef takes a rather distant third place, which is unfortunate, since it is the only truly cross-platform editor (I greatly dislike Java and it makes me biased).
With that said, there are other alternatives on Windows. Two option spring to mind immediately and both work quite well with LyX. The first program is an open source Firefox add-on called Zotero (http://www.zotero.org/). Zotero works very much JabRef in that it allows you to manage a library of citations, but it has the additional advantage in that it lives in the browser. When you search sites such as PubMed, Amazon and others, it includes a helpful icon to download the citation information from the webpage. It is also possible to import import PubMed searches and collections of citations (for example, I recently was able to download Neil Gaiman's complete bibliography from Wikipedia for a small book project that I am working on). Though I was skeptical of how useful the whole "research assistant in the browser" would be, I've found it is actually very handy. So much so, that nearly all of my citation management now happens in Zotero (with heavy duty backup provided by Mendeley, described below). Zotero can be directly used with LyX through the LyX plugin (https://addons.mozilla.org/en-US/firefox/addon/56806). I've been testing it for a few weeks now, and it seems to work pretty well. But I haven't done anything real with it yet. (My preferred solution is to generate a clean BibTeX file using Mendeley.) There are other advantages of Zotero as well. For starters, it allows you to use the same citation library with Microsoft Office/OpenOffice documents via a plug-in. This is something that is very important to me as most of my colleagues still continue to use Microsoft products. Additionally, it has an associated online service which can sync your reference library to multiple computers. While I've long done this with version control, the Zotero sync happens completely in the background and is more or less seamless. The second option is a program called Mendeley (http://www.mendeley.com/). Whereas the primary emphasis of Zotero is online research and citation management, you might think of Mendeley as a personal librarian for your reference collection. For this reason, it bills itself as "iTunes for reference papers". I use Mendeley to keep my PDF library organized and synced across my two laptops, work desktop and home desktop computers. The entire collection is indexed and searchable. It also has a wickedly cool in-text search that is very handy. However, by far the best feature of Mendeley is its ability to create highly readable BibTeX code. You can select citations to export, or you can have it automatically generate a BibTeX file for you. Because the code is clean, I've had no trouble using it with either LaTeX or LyX. Another very handy features is that it can sync its database with the Zotero database. This means that you can use Zotero to acquire citations and then have that information incorporated automatically into your Mendeley database as well. It's pretty slick. (As an aside, I've heard that sometimes getting the Mendeley sync to work on Windows can be difficult. I personally haven't had any trouble.) Mendeley also includes a Microsoft Word/OpenOffice plugin that works more or less identically to that of Zotero. The biggest downside, of course, is that neither program is a true BibTeX editor. But I've been very happy with the BibTeX created by Mendeley and Lyz makes it very easy to use Zotero directly from LyX. Thus, I've found that this doesn't concern me nearly as much as I thought it might. Good luck as you try out different programs. And if you find something that is better than JabRef, please let me know. I would love to find a good BibTeX editor on the Windows platform. Cheers, Rob Oakes