If you search the forums you will find that the most popular choices seem to be Bookends, Sente, or Endnote (not necessarily in that order). They each have their strengths and weaknesses. I’ve been through all of them, starting with Endnote and ending up with Sente. The latter is very good if you want to find and download pdfs over the Internet. Bookends is much stronger if you want to massage the database in various ways, and has some very powerful tools for that, but I find the interface a bit unpleasant. I’ve never really used Mendeley, so I can’t comment on it.
I, on the other hand, have never used Endnote or Zotero and until recently had never even heard of Mendeley. But when I needed to start work with bibliographic software, I tried both Sente and Bookends, and found that I couldn’t get on with the Sente interface, but was immediately at home in Bookends.
I think the choice between the two really comes down to interface preference, and if there is something that you need that one has that the other doesn’t. That said, there have been many upgrades to Bookends recently — perhaps since Martin moved over to Sente — which it seems to me may be addressing the aspects of Sente that Martin refers to, as well as a completely redrawn interface.
Both of them integrate well with both Mellel and Nisus Writer Pro, if you use either of those as your wordprocessor, and I’m sure with Word, though I have no experience of that, as well as with Scrivener.
Perhaps the only downside for you might be the cost, as neither is free. If you search for “Mendeley” in the forums, you will find a number of posts mentioning it.
Interested to hear that Bookends has an improved interface – I still have a licence for it, so I may look at it again. However, I should also have said that one of my reasons for moving to Sente is that there are some excellent AppleScripts that allow much better interchange of information with Devonthink than you can get with Bookends. I also found that some of the tools for messing around with the database in Bookends led me to waste time doing things that weren’t strictly necessary, but were an excellent way to procrastinate just to make things look prettier! That temptation is absent with Sente!
I ran across this thread, and I thought I’d mention that we’ve worked closely with Christian and Eric at DevonThink to create macros that integrate Bookends and DevonThink Pro. If you are interested in seeing how they work, you can use the Bookends demo (in case you don’t have a license for the current version).
Thank you all for your suggestions I am still struggling to find the perfect integration. I need to start my dissertation proposal.
I love the videos for DevoThink, but I haven’t the slightest idea how to use it.
I downloaded a demo for Sente - the screenshots look great, but I cannot get it to create a library, so I am still at the starting line there.
I am waiting for Bookends to un-zip right now, and it is taking forever.