I really like Qiqqa’s PDF bird’s eye overview, and REALLY like the multiple colors when searching for multiple words. Basically, the search and interaction with a single document is outstanding with Qiqqa.
Even more so, I was particularly tempted by the “Annotation Report” feature, which gathers all annotations and annotated chunks of a PDF into a single document for future review. Sente does something similar, as you may know, and I would really like to see such a feature in DevonThink in the future. Right now it is possible to reproduce this manually in DT by means of copy-paste and screenshot operations, all assembled in an RTF linked to the original PDF, but that’s far too tedious compared to the automation of Qiqqa or Sente.
I also admire Qiqqa for its cloud and sync capabilities.
Not to be ungrateful, of course: DevonThink does a lot that Qiqqa does not.