Docco is an interesting document management system that might work well as a complement to DevonTHINK. It's a Java application, using Lucene for indexing and searching, with plugins to handle extra filetypes. After installing the PDFBox plugin (as the older Multivalent plugin was giving errors), which just involved moving the whole unpacked folder into Docco's plugins directory, I fed it a directory of PDFs to index. Running a search then produces a visualisation of the papers at the intersections of the search terms, and clicking on a node shows all the corresponding papers in a list at the right-hand side: