You have covered the major ones already. The only other one that I also tried is JabRef.
I doubt that you will find the perfect solution across all of your needs. Each app has its own strength in certain functions.
Papers3 should soon have/already does have a desktop version of its new ReadCube/Papers hybrid.
—
JJW
I will take a look at JabRef today.
Thx!
I think Bookends is the best of the ones you’ve tried. I use it and it’s reliable for me. I have ~1800 refs in it. Don’t use the iOS client much at all.
There’s also some relationship between Mellel and Bookends. Don’t know what, but I’ve seen mention of it in Bookends promotions. Could just be an indie developer alliance. Mellel offers a bundle price.
Do not expect the link to DevonThink to be as well-developed as with Bookends. In truth, the only reason that I explored JabRef was to be in step with colleagues in the Windows world.
–
JJW
Having been a Papers 3 user I have now committed to ReadCube Papers. The academic subscription is cheap (made cheaper still with 40% off as a Papers 3 user), the desktop version is out (though not yet complete) and there is a sense of active development.I think the latter point is pretty important.
As one of the former Papers for Mac devs (before it was bought by Readcube), I can feel the pain.
Like others in this thread, I’d like to recommend Bookends. While Bookends may partly work different compared to Papers, it’s well maintained, continuously developed and has world-class support. And as the case with Papers shows, these things may be far more important long-term than any differences in features or usability.
Like Papers, Bookends 13.2 and above is nicely scriptable. This is a big plus IMO since it allows for customized workflows and also avoids lock-in.
As a case in point, for anyone considering moving from Papers to Bookends, I’ve written a “Papers to Bookends” script which exports all publications selected in your Papers 3 library to Bookends:
https://www.sonnysoftware.com/phpBB3/viewtopic.php?f=6&t=4360
The script will also transfer the publication’s primary PDF (if there’s any) and can also transfer the publication’s rating, color label, flagged status, language, edition, citekey, and “papers://…” link.
The PDF file’s annotations can be also transferred if you follow the steps given in the “Known Issues” section of the README.
For macOS 10.14 (Mojave) and above, you may need to copy the script’s code into a new ScriptEditor.app window and run it from there. Also note that, for larger libraries, the script may take some time until finished. But the script reports its progress, and it seems to work for many users. So this should ease the migration path from Papers to Bookends.
Hope this helps.
This might warrant its own thread, but since we’re talking about Bookends I figure I’ll put it here for now:
how do I do a one-click import from the web (Safari) into Bookends?
I’m used to Zotero. Managing papers in Bookends is stellar, but getting references in from Safari is far more cumbersome than Zotero’s browser extension. The experience is so much worse that I assume I’m missing something obvious.
Is there a browser extension or common script that simplifies getting references in from Safari?
I have Bookends watching a folder, then save the pdf from my browser to that folder. Bookends will import the pdf from there. Sometimes it will retrieve the meta data automatically, but sometimes I need to “autocomplete” the paper.
Ah, of course, the watch folder. I’m still hoping to make this one-click, but it should be trivial to write a script that downloads a paper to the watch folder in one-click.
Surprised that there isn’t a browser extension, though. It’s the killer feature of reference managers for many basic users.
There’s a bookmarklet. I wasn’t aware of it until I just went searching. Maybe that would help?
https://www.sonnysoftware.com/bookmarklet/bookmarklet.html
Huh. I want to believe I would’ve tried this before asking and found something wrong with it, but I have no memory of doing so. Huh. I’ll report back if this works! 
Aha. I have tried this before. It opens the Bookends Browser at the selected URL, but that’s it. There’s still a few more steps to get the thing imported—that’s like 500% the steps Zotero requires! 
But this has me inspired—surely there’s a way to macro/script this to be much faster. No such script is available on the first page or so of Google results, though. I’ll experiment and post back if I make any progress.
I have given up on dedicated reference software and now use Keep It to manage my academic PDFs (around 3000). You can organize PDFs using folders, tags, and colored labels. No citation integration with Word but I have found that the ability to use a modern, actively developed app that is feature rich on both Mac and iOS (supporting all the newest features) outweighs Word integration for me (I don’t even like Word). I have been using Keep It for several years (including for my current dissertation) and have loved putting the old reference manager apps behind me.
It uses iCloud as a storage provider, right?
From your experience: How well does the sync between iOS/iPadOS/macOS work?
And how easy would it be to export the data in a structured way, including text-notes/images/annotated PDFs?
How does the search work for you in KeepIt? Can you properly find what you are looking for in your large data set?
Right now I am using DevonThink 3 and Bear. Bear’s development is slow and I do not care about the web view they are allegedly working on. DT3, while the “AI” features are powerful, still has a massive interface issue. It has improved compared to the previous version, but it is still very unpleasant to use. And truth be told DevonThink To Go with the pastel color scheme and limited feature set isn’t really an app that you enjoy using, as well.
Therefore I am really looking for a solid alternative.
I switched from Papers to Bookends. The learning curve was a little steep, but now I have the hang of it I actually prefer it. More powerful interface, and much leaner and quicker than Papers. Plus, because it stores PDFs as Intelligibly names files in an actual directory (as opposed to a virtual disk like Papers), Spotlight indexes them to be searchable by content no problem.
Yes, it uses iCloud and has been quite reliable. I had one major syncing issue about a year ago; the dev was very responsive and we got it figured out. I was never been in a danger of losing data, sync just stalled on the Mac. Files can be organized by folders and by groups within those folder as well as by tag and by colored label. Files can exists in as many groups as you want and have many tags but can only be in one folder and have one label. It would be simple to export any data from the Mac and still maintain its file structure as all files are stored in the HD as real files and folders, not a proprietary database — just copy and paste (I don’t think you could preserve groups or labels, however, there is an option to sync tags with macOS’ tags which should preserve them). Search is robust with lots of options including saved searches, although a bit laggy on my 2016 12” MacBook. For my academic work and in-progress dissertation KeepIt has been great. The biggest improvements over Devonthink (I switched) have been the excellent interface on all platforms, macOS/iOS parity, and the removal of all the Devonthink features I never used. I also use Bear along side KeepIt — I use Bear for notes and KeepIt for materials (PDFs files and Text files as placeholders for physical books). KeepIt is quite adept at keeping notes in markdown, plain text, or rich text but I sometimes want to view my notes and materials totally separately so I keep them apart. I often, however, link a Bear note to a corresponding PDF in KeepIt using url-schemes (and vice-a-versa). Finally, I also use KeepIt as a pseudo-reference manager by storing a file’s bibliographic reference in the KeepIt comments field. Overall the switch to KeepIt from Devonthink has been very positive!
I have moved from Papers 3 to Papers 4 Readcube. It did not import all my data from Papers 3 and in the process deactivated Papers 3. The desktop Papers 4 app does nothing but scroll. The web based version is only marginally better. I regret the move. Can anyone recommend a better database?
I used Papers2 and Papers3 for years until they eventually broke. I reviewed all the players 12 months ago and went with Paperpile. I think it’s wonderful. Now available for the iPhone and IPad as well as via Google Docs or Word on the Mac. Superb for collaborative writing via Google Docs - no need to share papers, every one adds their own citations. Easy to share papers with others also. Its cloud-based paradigm feels very future proof. One month free trial and easy to import from legacy systems.
I would give Zotero a try, and if it doesn’t suit you, Bookends.