Referencing / Note Taking

I am in consideration to purchasing an iPad but was wondering if anyone can shed some light on my concern.

I work and am going to school so I do a lot of reading/writing and business plans. A lot of the reading I do now needs highlighting, note taking, referencing, etc so that I can notes/documents of all the info from various books. Is there an option/app that I can do all the note taking/referencing directly in the ebook on the iPad then have it transfered/synced on to a PC/Mac?

Thanks for the help in advance.