PDFNet has extensive annotation support, and annotations can be saved back to the PDF or be exported as a separate FDF or XFDF file. XFDF (XML Forms Data Format) is a format for representing forms data and annotations in a PDF document. It is the XML version of Forms Data Format (FDF), a simplified version of PDF for representing forms data and annotations.
You can get started by requesting a trial here: http://www.pdftron.com/pdfnet/mobile/request_trial.html. You may also want to check out the following snippets: FDF (http://www.pdftron.com/pdfnet/samplecode.html#FDF), Annotation: http://www.pdftron.com/pdfnet/samplecode.html#Annotation etc.