PDF reader that can save bookmarks & notes outside of the file

"I have the same problem. I have adobe pdf reader installed and I am using it to read some pdf books and I have no way to set bookmarks as to where I last left reading it or where I could refer to later on (multiple bookmarks in same pdf). adobe is projecting acrobat reader as optimized for reading, and there is no facility to bookmark specific areas in the pdf. I came across this solution in my searching but it works only for pdfs read through browser, not pdfs read as standalone:

http://oreilly.com/pub/h/2358

The ideal solution would be a program that allows bookmarking and stores such bookmarks outside of the pdf itself."