@iPersuade In case it’s of some help: years ago, there was a Readability (akin to Safari’s reading view) bookmarklet that worked well with Zotero, allowing Zotero to capture information that sometimes wasn’t available on the page when viewed without the bookmarklet.
Readability has gone the way of the dodo, but Brett Terpstra has a bookmarklet called Clippable that does the same thing.
(I wrote about the original bookmarklet for ProfHacker – yikes! – almost a decade ago.)
Thanks, I also discovered that Zotero has a good extension that works with the Brave and Chrome browsers, not so well with Safari. Thanks again!
I’m using Mendeley and have had good success with it. It is owned by the oft-chastised Elselvier, whom everyone has decided is evil for putting journal articles behind a paywall (SOME, certainly not all) and therefore like to dump on Mendeley as some sort of 2nd rate platform. In actuality it’s been rock-solid for my uses (STEM field) and has provided me years of utility.
This is why I consider them evil. I think they might have reversed this later, but I won’t consider them now.
I am in the hard science/engineering disciplines. I work mostly with PDF resources as the source references. I merge the citation information into publications using LaTeX. I have three reference management apps.
If I had no need to share with anyone else, I would likely dump Mendeley. FWIW, Mendeley has a new app in development that promises to focus back on the core vision of a reference manager (dropping those tools that give it a scientific warehouse + social media board feel). The new version will be opt-in for local (rather than opt-in for cloud storage). Given my (old-fashion perhaps) strong desire to remain local with my resources and only share when needed, this will be another reason I would move away from Mendeley.
If I had not already built a relationship with Papers3 (and did not thereby get a good discount on the upgrade to the new version), I would probably not continue with ReadCube/Papers. Its earlier invocations left me with the strong impression that it is does well in the medical fields (e.g. PubMed is its strong connection) and does poorly in the hard sciences. I defer that someone in the humanities/social sciences/business disciplines could speak to its utility in those fields. I hold on to Papers because it has a nicely done UI. It has probably the most intuitive, smoothly operating UI of the three apps that I am using. I would in fact go so far as to say that I enjoyed working in Papers3. Period. So I hope the experience my carry over as the new ReadCube/Papers app is developed.
If I did not have such a love/hate relationship with Bookends, I would drop Papers. I might make a rather vaguely-referenced and not intentionally crude to be cruel analogy about my experience using Bookends. If Bookends were a bathroom facility, to flush the toilet properly, you would have to face south, hold the light switch on, and recite the Lord’s prayer in Polish. But gosh, you can flush that toilet going clockwise or counter-clockwise or even straight down if you can create the right sequence of template codes (or AppleScript commands) in advance.
(Sorry but … I just came off an arduous weekend with Bookends and … Ask me to relate the story should we someday be chatting over a good Port in a gemütliche Kneipe in Berlin).
What is to love about Bookends? It is probably among the most powerful, feature-rich app for managing references. It is mac-Centric (when this matters as it does here). It has a very nicely done companion app on the iPad. You can split off your resources into individual libraries. It supposedly plays well with other “information management” apps on the macOS (DevonThink among the top, PDFExpert as well). It has one core team of two people who are passionate about the app (if not perhaps also a bit insistent about what I posit are its frustrating idiosyncracies). It beats Mendeley and Papers hands down in all of these positive regards, and it is these positive features that keep me returning to Bookends even as I struggle with using it.
I cannot speak for or against Zotero. I tried it many years (decades) ago. I was less enthused about its ability to handle PDF resources. Perhaps that has improved.
I also tried JabRef, primarily to find a tool that I could recommend to my team on Windows without the stigma of saying “Here is one to try … BUT I have never used it”.
On a closing positive side note, in the process of preparing a citation list this weekend in Bookends, I pulled up Obsidian in a split view. I made a great step forward even as an old dog learning a new trick about compiling a documented journal of my activities. While I was compiling references in Bookends, I was tracking the steps in Obsidian. I have yet to figure out how to drag+drop citations from Bookends in a way that makes them as hyperlinks rather than snap-shot references (I was probably not holding the light switch with the correct hand on this one). But, should drag+drop from Bookends to Obsidian be possible in a way that keeps a hyperlink reference, I will have a step forward in my own further exploration of Zettelkasten.
In summary, you won’t likely find a “best” by asking here or elsewhere. You will instead find a best by exploring a bit on the good ones that exist (and avoiding the over-priced ones aka EndNote). You seem to be off to a good start with Zotero and Bookends.
Hope this gives you some useful thoughts.
–
JJW
I’m using Zotero. I’ve never had a bibliographic system before. My use right now is almost exclusively for capturing info from PDFs of scientific papers on a variety of subjects including archeology, biology, genetics, textiles, animal science, computer science, database structures etc. etc. etc. I am combining with Obsidian and DEVONThink.
So far no issues but I’m in the early stages of using it.
I choce it because it’s open source, my data are on my machine and it’s got a lot of plugins and add-ons I can add to it if necessary.
I find Mendeley’s set of notation tools limited, so I often markup PDFs in another app (PDFExpert in my case) before filing it away in Mendeley. There’s an option to open sources already in Mendeley in another preferred app for markup, but this tends to be finicky so I make adding the PDF to the app my final step in processing.
I am assuming you already read Oogie’s dissertation on using Zotero and Zotfile
All of them suck. 
If only DEVONthink could handle citations… I keep my research library there because of it’s search/indexing features. Several citation managers allow you to import papers and search them, but they are inferior to DEVONthink.
Papers3: I like the citations (CTRL+CTRL) feature.
Zotero: nice (cross-platform) Word integration
Papers (online): very nice display of cited papers and similar papers
…and so on.
LaTeX is a thing for me (importing bibtex, also from clipboard), I don’t care about mobile apps at all, I’d like to have everything in one place instead of the weird Rube Goldberg-conundrum (Zotero+Papers3+DEVONthink+etc) I am using right now.
I struggle to name a “best”, with some effort I could name a “least worst”. Might me Papers3 for me if I had to stick to just one.
I use Bookends and I’m really happy with the application.
There is a feature overload, but once you get your head around the interface it’s a fine application for the job. As other have said, when adding a new paper/article/book you can search several online directories (e.g. Google Scholar, Google Books and lots of academic repositories), and have all the details automatically filled in. I’ve yet to come across a publication that can’t be auto-filled.
The developers are also really responsive. Whenever I’ve had an issue they responded on the same day and fixed it.
Your bathroom facility analogy raised this post to a whole new level, I’m still laughing! 
The information you provided is also helpful and appreciated but I’ll remember the analogy longer, thanks!
You’re right, that works perfectly. I had wrongly assumed that the best approach was importing from Amazon as I was able to do with Zotero. Thanks for the re-direction. I’ll continue giving both apps a test drive.
Thanks everyone for the great input. You have been a tremendous help. After several hours of testing I have settled on Bookends. I believe it will best meet my needs.
I have a question for experienced Bookend users.
It seems as though one can use the citation manager with Pages–see screenshot. I cannot figure out how to invoke this in Pages. Do any of you use Bookends with Pages and if so, how do you invoke it? I have it working fine in Word, which I can use, but I’d prefer to use Pages if possible.
Thanks again everyone!
I believe in this case you would use what they call Floating Citations to insert a temporary citations, which can then be converted to a real citation when you “scan” the document.
You assign a key to invoke Floating Citations in the Bookends preferences. The when you double-tap, say, Option, the citation window pops up and let’s you search for a reference.
Thanks @JohnAtl, I’ll give that a shot! I use the end of the year to refine/revise my workflows and apps. I’m feeling very good about my revisions and moving forward into next year. Happy New Year to you.
Happy New Year @Bmosbacker!
I’m taking a note from you and deciding on a project and task management system for the year.
This past year I’ve used five, including the current one.
Sometimes I think we make things too complicated! To prove the point, I just posted this new workflow. 
