I switched from Zotero to Mendeley last year at a friend's recommendation. You can import PDFs (or have it watch a folder for PDFs) and if the PDF is searchable, it'll index it. Then you can search through your entire digital reference library in one go. I use the notes field and export to BibTeX for writing up my papers. I think Zotero handled images better (and a lot of my research is in the form of "stare very hard at a Raphael painting"), but overall I'm happy with it.

I'm not really an academic. I'm an amateur experimental archaeologist, and I've gotten a reputation among others in my region for having good papers to go along with my experiments. Consequently, other folks doing experimental archaeology have started saying things to me like "I know somewhere in my bookshelves there's evidence for all the stuff I did, I just can't find any of it to write up the documentation!" I keep recommending Mendeley.

Certainly it's more useful to use while you're researching than to try to go back and fill in a bunch of stuff you read before and find where it was in the book so you can have page citations on your notes. That's just a reason to start using a research manager sooner.

Not software related, but you also might find handy: I've glued library pockets into the backs of some of my books. I make secondary indices for things not normally found in the index (for instance, listing all the figures in a given book that show a Spanish farthingale versus a French farthingale).

I find some people love them to death.

I personally use EndNote. The biggest draw back for me, is that it sometimes plugs in the citations in weird formats. There may be some settings I can fiddle with but I have never figured them out: for instance French books often only capitalize the first word of a title- but when I use EndNote to plug in a citation it likes to capitalize all of the words.

So instead I will often just copy and paste the full citation from EndNote the first time I use it, fixing anything I need to, and then type the short citation myself after that. Of course Journals and so forth often have their own slightly peculiar citation styles and formats and some specify that they don't want embedded citations from citation software- I suppose they might be harder to reformat. So thats another reason why I don't use their plug and play ability really.

What I absolutely love- and what I really use endnote for- is as a database for storing my collection of PDF articles and books, as well as syllabus from different people, conference papers- crafting different collections of PDFs and citations for specific research projects. I love using EndNote for all of this, it really helps keep 90% of those sorts of files together and in one place thats easy to search and sort. I have absolutely no idea how I would manage all of these files without EndNote, its simply central to keeping everything together.

I have seen Zotero, and know a few people who use it too, it basically looks like the same to my eyes. I have no idea its capabilities, but I imagine them to be roughly comparable. I haven't experience with many other systems.

The one thing I don't use EndNote for, is scanned archival material. I wish I could, but some of the files are just too big and the citations too awkward. For those I still use folders and maintain a master spreadsheet to keep track of the files, keywords, and citations. I do use EndNote for lots of published archival material- that tends to be easier to enter into the database for searching later one.

I use papers to organize PDFs. On paper (sorry), it is amazing. I went with it because it has pretty much every feature I wanted. In practice, I discovered that it slows to a crawl once you have a lot of PDFs in it, which of course you don't really discover until it is too late. If I could go back and start over, I've poked around Zotero, Mendeley, and Together, and all seem OK. TLDR Avoid Papers if you have a collection of appreciable size. Its great if you have only a few dozen.

Every time I see someone asking about reference management software I have to jump in and recommend Zotero. Heres the condensed evangelising:

1. Zotero operates on an "online, webcentric, information everywhere" mindset. It lives in your browser, it allows you to save all sorts of files from the web to your citations, and it syncs your citations/attachments with the cloud and your other devices. Integrating with Dropbox/Onedrive/Google Drive is super easy - sync your citations through the zotero cloud, and sync your pdfs through dropbox. Easy. Makes using multiple devices with the same ref library super easy.

2. Its easy to get stuff into Zotero, search within your library, and export stuff out of Zotero. You can save citations with their corresponding articles with a single click on webpages that have that data available. You can drag n drop your entire pdf collection into Zotero and ask it to retrieve the metadata and give each pdf a citation (It uses google scholar in the background to do this which has been reliable and very accurate in my experience). You can ask it to watch a folder and automatically add pdfs that get saved in there. Search your whole library easily, pdfs can be indexed, keywords can be added to citations automatically.

3. In text citation and bibliography generation are super simple. When writing a document either cite as you go from the zotero interface, or just type the citation in. At the end, one click bibliography generation, or select sources inside zotero to form your bibliography. Select from thousands of reference styles from the zotero style repository - mendeley piggybacks off of this repository too.

4. There are extra plugins that add even more functionality to the core experience. Zotfile adds extra options for file management, Zutilo allows you to carry out misc operations in batch mode, some plugins integrate with other software, one allows you to attach how many google scholar citations each reference has etc.

5. Simple but powerful workflows - When you save a citation, it automatically downloads the pdf, renames it based on citation data from filters youve chosen i.e 'Smith (2005) Article title.pdf', moves the file to a folder hierarchy which is generated based on filters you decide i.e Journal/Year/Author/Article.pdf. Attachments are linked to the citation - never bother with file management again, simply double click the citation to open to the pdf, right click and show file to open the file location.

Basically, zotero is awesome and in my view it blows the competition away easily. The best bit is the sheer amount of time saved, and the ease of organisation for your library of refs. I strongly suggest you head over to the site and check out the intro video and the quick start guide. When you're ready, check out the Zotfile plugin too, super handy. Another great guide is Mastering Zotero.

Let me know if you have any questions.