The comments you make in response to, and including @superboyac's
comments bring some of the MS OneNote Notebook
ergonomics and techniques to mind.
- earmarking: though "earmarking" is probably not the correct English term for what is being suggested (I think making a dog-ear as a bookmark might be what was intended), you can meet the description it is given in the above comments by the use of "Tags" in OneNote and also with typed or handwritten notes added anywhere on the page being viewed.
- finding stuff: you can automatically index/search and/or make a hyperlink for any word, phrase or image in the reading matter or comments (hyperlinking being similar to a Wiki) and index/search OCR'd text in images. The reader can also easily add copious notes at the hyperlink page - which typically could be (say) in another Notebook, away from the actual hyperlinked text, if required.
- display: the Notebooks can be viewed in a 2 or 3-pane display (Notebook/Section, Page/Subpages, Page Content (showing any notes or images added by any user/reader)
On the subject of a need for a book-like appearance:
In terms of priorities of requirements (e.g., A=Mandatory, B=Highly Desirable, C=Nice-to-Have) I would suggest that this is a C
- i.e., more of a touchy-feely thing to help people get over their natural resistance to the transition from an analogue to a digital medium. So it could be a distraction from meeting fundamental requirements of the A + B categories. Trying to meet a C requirement could turn out to be a potential bottomless pit for development costs and with ultimately very little real added value.
If you are focussed on PDF files, then you have a relatively narrow focus on one of several restrictive generic or third-party technologies, over which you have no real control.
However, if you are seeking to improve that technology so that reading and making notes on the PDF digital medium becomes at least as easy as and as ergonomically efficient as an analogue medium - preferably better in both cases - then you are on a relatively well-trodden path that was arguably kicked into the Big Time by the advent of things like the Nook or the Kindle - though both are seemingly designed as proprietary market entrapment devices.
However, you are arguably amongst friends/helpers who may have gone before you, in the form of the developers responsible for the development of reference/reading management systems - refer for example:
If you have not already done so, then I would suggest that having some examination/trial of those free systems, and some collaborative dialogue with their developers and about their forward plans might be very useful - even synergistic in effect - and might even help you to avoid re-inventing the wheel in some areas, to some extent.