There are really two distinct processes
Annotations not possible on ipad, new verion end 2012 will allow this.
Has the whole process, well thought out. No version for ipad as of nov 2012.
http://professorphd.com/post/20262981851/qiqqa-review-complete-workflow-for-research discusses the use of qiqqa, also with iannotate on ipad. Says that qiqqa is the only one that has an annotation report.
Has the whole process, incl mindaps ased on annoations from pdf
Full reference mgmt suite. This has an app and versions for mac and win.
Full reference mgmt suite. Has an app and a version for mac, but none for win
Enables taking note snippets, sorting them and eventually putting them together in a text document. No tags.
Overview of apps to make Annotations on the ipad
Another overview, about ipad apps for pdf annotation
Another post from Joachim Scholz, comparing sente and papers.
Professor phd, made by a phd student who uses qiqqa and ipad. Asked him how he integrates the two, and how he tags notes if using another ipad app for that.
Audio annotation tools
2 ønsker: kan gemme hilights og kan lave en annotation report