There are already some threads about note taking:
Annotating pfs & powerpoints
How-to Optimize OneNote on Surface
Please use the search function the next time - and with keywords like pdf notes (pdf has only three letters and will be ignored, so the search results wouldn't be helpful) you could useto get some more helpful results.Code:"pdf note"
I'll close this thread, if you have any further questions or found an new app, just use one of the threads mentioned above