Here are the requirements, the users needs to be able to view uploaded PDFs in the browser. They need to be able to add notes to the PDF and save the updated PDF to the ser
You can use either PDFSharp or itextsharp to create annotations. Haven't tried PDFSharp annotation but iTextSharp does work. You'll have to handle the editing on the server side. probably copy the file to a temp folder edit it and save it back.
You'll find itextsharp at http://itextsharp.sourceforge.net, annotation example: bottom at the page http://itextsharp.sourceforge.net/tutorial/ch03.html
pdfsharp: http://www.pdfsharp.net