Last year I finished my PhD thesis. However, I am not entirely sure that I used the most efficient workflow for academic research. I wanted to go risk-free, as I had a tight deadline and nothing could go wrong. I worked on a Windows environment, and I used Microsoft Word 2010 (the 2013 version had not yet shipped at the time) for outlining and writing, Endnote (for citations), Adobe Reader (for PDF reading) and a combination of dtSearch, Qiqqa and Archivarius (for PDF search). Not the best workflow, perhaps, but I decided to play safe with Word + Endnote. Now, I am on a Mac, and I would like to streamline my workflow. I am tending to use the following applications, and I would like to know if you would suggest any alternatives or if you would recommend me to take a second look on any software I may have overlooked. I would like to know what do you use. DevonThink Pro Office for PDF indexing and searching. It has a clunkly interface, and may be overkill for the task, but it is fast, searches all my documents and organize the results. Plus, it highlights all the searches. And also has OCR for those PDFs that contain only images. I found it to be good. I tried Together, which has a very nice interface, but it could not organize well the results nor highlight them. Yojimbo highlights the search results, but cannot display them hierarchically. Ditto for EagleFiler. Skim for annotating PDFs. Although I think Preview or Adobe Reader are also up to the task, and I don't see much difference between them for this. Is there any? Circus Ponies Notebook for taking notes, collecting information and basic outlining. It may be a little outdated (the version 3.0 dates back from 2008), but looked and felt nice. In addition, it can hyperlink to other sections of the document, which is nice. I also tried OmniOutliner Pro, which is in version 4.0 now, and has a better interface, but, although I feel it is a very competent outliner, it may not be so good at taking notes. I may be wrong, though, and may be skipping a brand new and fully-featured piece of software in exchange for some old and outdated software. There is also Microsoft OneNote, but I felt it underpowered compared to the Windows version. Scrivener for writing. It looks and feels like a very competent piece of software for academic and structured writing. The draft view is very useful, and I can see all footnotes at once (and not only those that fit on the page). It is awkward not knowing how the page will look like in the end, but I will have to get accostumed with that. Microsoft Word would be my second choice. It is very fully-featured, but Microsoft seems to constantly neglect the Mac, as the Windows version is far superior and there are no signs of release of the next version. LibreOffice Writer and OpenOffice Writer seem like cheap Word alternatives and I rather prefer to use the original. Mellel is nice and solid, especially for academic work, but is bad for converting files to Microsoft Word format (which is the standard that I must use). Plus, its interface does not help and seems to be clunky. Nisus Writer Pro is good, but, again, to use a Word replacement, I would rather go with Word itself. I see no reason for using Nisus instead of Word. Apple Pages is OK and has a very nice interface, but it lacks features and does not even support cross-references. Sente for citations. I need to cite in footnotes in my field of research and Sente seems to support that. In addition, I found the interface to be good and the system of citations to be straightforward (a "cite" button inside the program). I tried Papers which is on a very criticized version 3.0, and the interface is also very good. However, the system of Magic Citations, although beautifully designed, seems to get in the way of doing things. (Why is so many people complaining about Papers?) Bookends is also nice, but it does not have exactly the best interface nor the best citation system in the world. Endnote integrates well with Word, but the system seems outdated. Zotero is nice, although it does not have the best interface; the citations seem to work well with Word, but not with too many programs. I have yet to figure out Mendeley and BibDesk, but I guess neither of them will be as good and streamlined as the others. Microsoft Word for final review of the draft. I could use Apple Pages or Nisus Writer Pro or LibreOffice Writer. However, as I will have to send the article on Word format to any publisher, or share in Word format with anyone else, I would prefer to go with the original. So, what do you think? Anything missing? Agree or disagree?