I have been working with Zotero for some time now and seen it grow over time. I have run into a few issues of workflow by using Zotero. One is reading/reviewing/annotating PDF articles added to my Zotero library for active and future projects. The second roadbock is citations in other programs that are not currenlty supported by Zotero plugins. Still have not solved the latter, but the first is coming along.
A few workarounds have been created, including a plugin for Zotero that round trips the PDFs in Zotero out to Dropbox, which can then be annotated through any PDF reader app that supports Dropbox sync on the iPad. Later the plugin on Zotero can check that synced Dropbox folder to pull the annotated PDF back into Zotero. The downside is it requires forethought in order to load the required PDFs into Dropbox and to sync them back later on. Not ideal, but not too bad. The other nice thing about this is it can pull the highlights and other notes into a text file.
Another option is Zotpad for the iPad ($9.99 currently in the iOS App Store). Mark Sample over at the ProfHacker blog recently did an extensive review of Zotpad. It has come a long way since it was originally released, including being able to sync over-the-air with the Zotero server, your own WebDav server or even Dropbox. Currently, Zotpad does not allow to make annotations within the app, it does allow you open your Zotero PDFs into other iPad apps and then when finished important back into Zotpad. Again, not perfect, but getting better.
These two issues in workflow have made me look around for other citation/article management systems. I have been playing with Papers 2 from mekentosj.com and their iPad app. Without going into the full review, the pluses currently for Papers 2 over Zotero is tight intergration into the OS X and the ability to cite in any writing application. The minus is Papers 2 app only can sync with its iOS app while on the same network, but the iOS app does allow annotations in-app and those annotations/notes can be pulled out as text files.
EndNote used to be the only option for citation. Between Zotero (open source) and Papers (for-profit app developer) no one should need to look at EndNote to get serious work done in academic research.
Currently Zotero is limited Word and OpenOffice and does not support citing sources in other programs such as my two favorite writing environments–Scrivener and Byword. ↩
I plan to work on a larger review of those two citation/article management systems in the future. My final choice is still up in the air at this point. ↩