Zotero

Zotero is probably the “gold standard.” Its recent design update did little to make it look more appealing, but it does a lot of things very well, and the things it does not do are implementable as plugins. BetterBibTeX is more or less a mandatory additional install. Does most anything you’d need a citation manager to do for you, including a “Notes” function that will soon also export to valid :octicons-markdown-16: Markdown.

Paperpile

Paperpile is web-only and integrates exclusively with Google Docs. Some academic institutions and universities have gone this route, and if that’s where you want to keep your citations, it’s $3/month for academics.

Mendeley

Mendeley is owned by Elsevier. Yes, the people making money from other people’s work, selling them to those who, with their taxes, already financed it. It’s OK for light citation management but it, does not have automatic export and you’re forced to have an Elsevier login for it.

Papers

Papers by ReadCube used to be a Mac only citation manager with somewhat useful tools. It does what it says on the tin, including web import, but it feels sluggish at times. Papers can supposedly maintain an automatic export to .bib for LaTeX projects, but I was not able to get that running on Mac.

JabRef

JabRef is a truly Open Source citation manager with many great features. While it does not have an auto-export on update (“Keep Updated”) function, it does save its library in BibTeX, thus making it somewhat easier to work with in applications it does not provide a connector for.

Endnote

EndNote is the Ferrari of citations managers. And like a Ferrari, it’s harder to drive, it’s costly and does way more acceleration and top speeds than are possible most anywhere. Or, to drop that tired comparison: EndNote is great, but unless you’re spending all your life living inside a citation manager, it’s overkill.

For 95% of academia (students, profs) and 100% of writing that requires citations but doesn’t aim to do a massive meta review once a year, other solutions are available and better.

One advantage of EndNote is its support for Apple’s Pages. Apple charges a pretty penny for anyone wanting to use Pages’ API, and only an expensive app like EndNote can bring this. On the other hand, few academic institutions use Pages, the missing support for figure and table captions alone means it’s close to unusable.