title_body: Annotation of non-Amazon books on Kindle Paperwhite
upvoted_answer: Update 2018:
  Got an epub book? Best way at the moment for most qualiity and support is renaming to .txt (or png?) and sending to kindle email adress with convert subject (doesn t even need convert subject here? ;  anyway better than calibre mobi conversion way). This way (direct) epub conversion is supported although it s officially not.
  
  
  
  TL;DR (today's environment)
  
  
  Yes, you can annotate (pdf and azw...)
  Yes, on formats like azw.. (you can convert via amazon upload "convert" as email subject; or calibre) you can extract your annotations via clippings.txt on kindle paperwhite, or by sharing it around your devices (amazon upload) and export with android kindle app.
  No, using pdf, getting the annotations outside seems to be difficult, you can annotate though, but for me without being able to extract them, this is a bit sensless (there are also no normal pdf annotations, like you know from adobe reader). As PDFs are the onle way for some documents (magzines, math formulars?) this is annoying. Any solution is appreciated! 
  For Amazon bought books just use: read.amazon.com/kp/notebook (or the azw... possibility explained above)
  
  
  
  
  As I'm highly interested in reading PDFs on my kindle paperwhite 3 (the recent one), as I want a perfect reading experience (eInk/no bright display and high resolution) and the kindle paperwhite gives me that. I experimented with my kindle fire and my paperwhite, so far my insights for the kindle paperwhite are (they correspond to todays possibilities, when something changes, feel free to comment):
  
  
  You can annotate converted ebooks and pdfs
  The problem is how to get the annotations outsite of the kindle paperwhite
  
  
  There seem to be 3 factors:
  
  
  Which software version (kindle) do you have?
  How did you transfer the data to your ebook (by usb or by amazon uploading)?
  Which format do you use (pdf or epub or azw...)?
  
  
  The software version decides how the notes are stored on the kindle. It seems to be that in earlier version notes where stored in an "mbp" file format, which could be read with the right software. But amazon changed that to "mpb1" (I don't know, if it is possible to read that). (I tested everything with today's recent kindle version 5.8.10.)
  
  The transfer type decides if your uploaded document (only the document, didn't say anything about annotations yet) is distributed to your devices. It is distributed if you upload it via amazaon (e.g. with send to kindle via email), with USB it is not. 
  
  The format decides if your annotations are synced around your devices. This obviously only works, if the document itself is synced (uploaded via amazon). So you need to upload it via amazon and use an kindle compatible book format to share your annotations (pdf won't work).
  
  temp TL;DR:
  
  
  If you want to just share your document around your devices (not annoations), use amazon uploading.
  If you want additionaly to share the annotations also use amazon uploading but use a compatible file format (not pdf), easiest way is, writing "Convert" as the subject when sending the file via email uploading.
  
  
  Sadly: https://read.amazon.com and also https://read.amazon.com/kp/notebook? (shows your annotations in the browser) won't work with that methods (also the windows kindle application!). They just work with amazon bought books, as I see it.
  
  For me, this is very unsatisfactory as I don't just want to have the notes on the kindle reader app or on my kindle paper white, I want it to be on my pc! Reading app for pc would only be second best option, but as I said, it doesn't work like i said in the paragraph before. 
  
  So I experimented further. 
  
  
  paperwhite usb to pc: There are many formats, somebody may try to open these: .apnx, azw3f, azw3r, mbp1, mbs, pds, pdt. I didn't really, would be great if somebody finds out something.
  open the clippings.txt under documents. There you can find the annotations of kindle books formats (azw... and so on, but not pdf) (can also be synced files), 
  
  
  Sharing the notations via kindle itself:
  
  
  The sharing options on paperwhite are shit, you can only share a single annotation at a time, and you can share it with facebook and twitter - facepalm.
  The sharing options with the android fire kindle app are good and much better. But this only works with formats like azw..., it does not work for pdfs.
  
  
  The pdf annotation extraction/export seems to be difficult. This is very unsatisfactory for me, as some documents (math formulars?) and magazines can only be read properly as an pdf. I appreciate any solution in this area!