Advantages of EndNote over BibTex, if any

I don't use Endnote, but I frequently edit Word documents whose bibliographies have been prepared using it. The following contains much extrapolation from personal impressions.

They have different ideas about use. Endnote is a bit more like Zotero than traditional Bibtex, stressing its access to official abstract and bibliography servers, with many users who have never either edited a bibliography entry themselves, or felt that they are maintainers of a bibliographic database, because they haven't felt the need. The idea is that that the professionals have taken care of the massive Endnote bibliographic database, so that you don't have to worry about it. This idea of being taken care of is supported by the work that the Endnote producers (recently Endnote was acquired by Thomson-Reuters, now one of the world's two giant news & professional information agencies) have put into cultivating a dialog with the major style guides, such as APA, so that their output is accepted by the authority as being in conformance with the official style.

The results are pretty good, but not as good as users expect. Very commonly I received manuscripts from clients who say I don't need to look at the bibliography because it was prepared with Endnote. I then look over the bibliography to see if I find any errors. Inevitably I do, occasionally serious ones, which I report back to the sometimes very surprised client.

Endnote allows export to Bibtex format. If you do so, the promises about conformance to style guides become worthless, as the Endnote representation of reference metadata does not cleanly correspond to Bibtex's. I have the idea that the same problems will apply if one tries to convert Endnote's format into the new Word 2010 reference format, but I have not confirmed this.

Bibtex is free. The standard Endnote package has an RRP of $300, and will require fairly frequent paid upgrades for most of its users.

I've had some issues with EndNote over the years, some of which have been addressed in more recent releases or perhaps 'go away' if you switch from .doc to .docx Word files. My boss wrote a paper about 18 months ago with a large EndNote library and sent it to another academic for some editing. This all worked fined until my boss wanted to alter the references a bit. Our colleague uses OpenOffice, and although it preserved the look of the references it lost the library element. So they all had to be re-done by hand. As I say, that was a document in .doc format, and we might have been better in the more open .docx format.

I've successfully used BibTeX4Word in the past, as it lets you use a BibTeX database and style file with Word (provided you are reasonably careful). For me that's always been a good balance: I have to use Word at work, but prefer to have my references in BibTeX format.

Charles is quite right that the big selling point for EndNote is the idea that the user doesn't have to worry about the 'bibliography management' side of things. However, I'd also agree with Charles that this doesn't quite work out as you'd like. At least in my field (chemistry) we reference stuff that is in press or has complex notes to add to the references. Nothing automated is that good for these, so whatever approach is uses there is still a lot of typing to do.

Endnote is still the standard in several fields and some people are forced to use it because they have to collaborate with other Endnote users. Still, my advice is: If you don't have to use it, stay away from it.

Endnote is a buggy and overpriced piece of crap with serious limitations. I haven't used Endnote for quite some time and just downloaded the latest trial to have a look at it, and guess what: It still has the style editor it had 15 year ago; if you're in English speaking hard sciences, this will probably do, but anything a bit more advanced is a problem. Modern systems like CSL (Zotero et al.) or biblatex are incredibly more powerful.

Many of Endnote's shortcomings have been known for year, but Thomson Reuter's support boils down to a regular $99 bug fix release.

Oh, and it looks like its BibTeX exporter is still broken by default.