Are there any PDF and/or ebook readers (for epub, mobi and/or lit formats) that allows you to "add" to the text/page in a way you can retrieve next time you open the text? Things like (margin-)comments, "sticky-notes", corrections, underlining and highlighting, … i.e. things you may do in a "real" book. It would probably be best if the original file was left untouched.
I'm using a PC with Linux (Ubuntu), so I'm mostly interested in a reader for it - where mouse and keyboard is used for highlighting and notes. However if there are programs for tablets doing similar things (but perhaps with touch-and-swipe or pen interface), I'm intersted in that too.
It's just that I got lots of ebooks I'm reading (mostly PDF), and it would be great to leave comments and highlighting - without having to print-out a hardcopy.