http://www.mendeley.com/ -- the best free tool

Big thumbs up for Mendeley. The most important features of Skim (high-lighting, notes), plus bibliography, intensely cross-platform, and in the cloud. I'm using it on an iphone, ipad, mac, and an NMCI Windows XP box (supports proxies). Oh, yeah, it integrates with Zotero.

I use several machines (running Ubuntu), so Mendeley is nice to keep everything synced. Also, it works well for sharing citations with other people.

Even though you can store papers on Mendeley, I actually keep most of them on Dropbox.

Is it better now? I have tested it before but it was too buggy for serious loading (PhD thesis), although I liked very much the interface and features.

The in-application browsing experience is pretty lame on OSX and Windows, but 'open externally' works great.

The iOS app is almost there. Once it has sync like the desktop (right now you have to individually download each!) and supports opening in GoodReader so there's good display and editing, it will be useful. But for now, if you want to do any practical device reading, you'll probably want to pull it down on the desktop and transfer into GoodReader via iTunes.

Papers is quite nice (http://mekentosj.com/papers/). Caveats: Mac/iOS only, not free.

I've been using this for the past 4 years. They've got a nice iPad app that includes highlighting, but unfortunately their desktop app can't handle highlighting yet. :(

Their priorities are a bit backward. The desktop app has been surpassed by almost all other competitors mentioned here. Sad. Used to be great.

I use Papers with Dropbox for syncing my library. Works pretty well as long as you don't try to run it from several computers simultaneously.

I'm pretty happy with Papers, too, though I must second the other post about the Mac app being related to second class status. There has been basically no feature improvements (highlighting, for crying out loud) since 2008 when I started using it. Now I use Skim for annotating instead, which is a bit lame since you can't see the annotations within Papers, but the advantages outweigh the disadvantages.

Its download interface is quite nice. You can follow links in IEEE or Web of Science and d/l a lot of related papers + metadata painlessly. This makes it really good for coming up to speed with new subject areas.

Calibre... for me solves all problems

I keep Calibre's library on Dropbox, and so also solve the problem of keeping my library in sync between different computers.

I updated Calibre for the first time in quite a while recently, and I'm really liking the new interface.

that looks interesting. thanks for the tip :)

I have been through all the apps mentioned here and settled on Sente (www.thirdstreetsoftware.com). Very powerful, does all the biblio/citation thing if you need it, as well as the visualization part that Papers does. It is not as polished as specific tools (such as a Papers/Endnote combo), but I find it nice to store all my pdfs in one place, automatically adding meta data through Google Scholar, Pubmed or whatever, and commenting/highlighting in the same application. There are also some very good applescripts to export notes to Devonthink and implement a citation database à la Steven Johnson (http://www.stevenberlinjohnson.com/movabletype/archives/0002...). My main library also sits in Dropbox, and is always accessible even when I am not at a Mac.

I started using BibDesk (http://bibdesk.sourceforge.net/) with Dropbox just last week and have been pretty happy with it so far. I don't have anything, yet, for books, but I suppose I could just write BibTex entries for the books and be done with it.

I'm using Yep! for organizing my Documents via OpenMeta-Tags (they're synchable via Dropbox). Yep uses Spotlight for indexing Documents so you're able to find fast. The cool part is that you can have a second organizational structure on the data level. (You're able to put PDFs where you need them, eg. project folders, and still find them in Yep!) For bibliographys and stuff like that I use Sente. I search for all my PDFs with a certain tag in Yep and just add them one by one to sente. This works great for me. Btw: Sente is also able to create a synced copy, which is great if you have different macs (like I do) and working longer on a paper or article.

I tend to keep my e-books and research papers in different piles in one sense. Calibre handles the e-books better than just about anything else out there. For research papers I use DEVONThink. I tend to be a bit of a research paper pack-rat and DT makes it easy for me to find what I want in my huge slushpile of PDFs. The current DT iOS app is a bit of a work in progress, but until it gets to the same level us usefulness that the desktop version of DT had I can easily dump papers for mobile reading via the Dropbox->GoodReader path.

I use BibDesk to search for and organize research papers and Skim to read them (both Mac OS).

I like to write company-confidential notes on the papers, so I don't sync them anywhere external, so as to comply with security guidelines.

That ends up meaning that 'sharing' papers means just emailing the PDFs around.

Yojimbo (http://www.barebones.com/products/yojimbo/) plays quite nicely for this sort of thing, and works with Dropbox too to keep your library synchronised across multiple machines.

CiteULike (http://www.citeulike.org) for papers. I like the ability to upload PDFs so that I don't have to keep jumping around paywalls every time I want to refer to an article.

Mendeley to organize, Xournal to read + annotate, git to store, share, sync.

The git part somewhat laborious, but until SparkleShare gets released officially that's what I'll work with.

I should add that I arrived at Mendeley after Bibdesk, after Zotero.

Zotero

Mendeley integrates with zotero, fwiw.

ibooks app on the Ipad with Dropbox ... as long as its in pdf format you can just put it in dropbox and add it to ibooks from there. love it.

bibtex + file system

I'm using CloudApp for most of the sharing and then Dropbox for bigger files. I really want to recommend Papers. It's really nice and keep me away from the documents explosion.

A folder called Bibliography with files named as follows: "first_authors_last_name' 'year_of_paper' 'title_of_paper.extension"