I’ve been using DevonThink as I work on my PhD dissertation. Its a great product that serves most of my research needs.
Like many academic users of DevonThink, however, I use Zotero as a tool for collecting and managing citations. Given the ease with which Zotero can pull both citations and PDFs of journal articles from sites like JStor, I’m keeping journal articles in Zotero.
It would be really great if the developers could come up with a way to automate the indexing of one’s Zotero library into DevonThink. I know there was a third-party script developed by kmlawson, but this no longer seems to work (not even for him, based on my recent conversation with him about it).