The only other contender with Scrivener is this Open-Source Research Organiser called DOCEAR.

The only other contender with Scrivener is this Open-Source Research Organiser called DOCEAR. Essentially it'sa Mind Map program based on Freeplane in which you insert your research as nodes in the map, and later write your research paper usinga similar system.  May have uses, but when I last tried it it seemed mind bogglingly difficult to get used to.  I suspect that Scrivener can do similar things, but using its organiser instead of a mind map.
#scrivener #docear #research  
http://www.docear.org/software/details/