The point is to make things frictionless and seamless. Anything that takes even 2 steps away from natural flow, I am out. I am predominantly a laptop user, so it's driven from that point of view. Although I ll place android options also in this thread.
I am a mac user, so this is mostly driven by mac apps. Please do pitch in windows alternatives. First of all, this app called ClearView (macupdate.com/app/mac/47325/…)
It has tabbed reading like a browser. Once annotated, you can read the highlights on a separate notes section.
It has tabbed reading like a browser. Once annotated, you can read the highlights on a separate notes section.
This is what the app looks like. You can see the notes and annotations separately, bookwise, in a separate section too if you want to quickly glance into the highlights alone. 
You can export notes as RTF or go to PRINT NOTES in the menu, and save as PDF using the ensuing option. This is great for many evernote users as you can save and index pdfs within evernote system. But for roam/obsidian users, PDF is a no-go.
The best option is to select all the highlights in one go, copy paste into a markdown file as clean text within obsidian or within Roam in however format you want.
The next app that's super cool is HIGHLIGHTS (@highlights_app). highlightsapp.net
Check out the formats available for export. They have recently added support for @BearNotesApp too.
Check out the formats available for export. They have recently added support for @BearNotesApp too.
This is what happens when I create a highlight. The rightside preview changes into a markdown editor where the annotations are automatically added in markdown format.
You can view or edit notes as per convenience. Once you're done reading a book, you can bulk copy paste the entire annotations markdown to @obsdmd or @RoamResearch.
These are not the only features. If you look at the app page, they have listed the exhaustive feature list. Check it out and I think this could be a wonderful application to use for you to read, annotate and do your research related activities, take notes, and convert to md.
PDF Expert software is a recommended one across mac, windows, etc., it can export notes into txt, markdown, and html. But the formatting is so ugly that there will be a lot of clean up effort required. Not worth your time.
For those who can't afford to pay for a software, there's this beautiful free piece of software called SKIM. It can open only PDF files. Using this READ NOTES option, you can convert all the pre-existing annotations in the pdf from other softwares to this app's native format.
You can view all the annotations on the right side as you can see in the image. You can just do a "SELECT ALL" in that annotations section, ctrl/cmd+c and paste into your obsidian or roam editor. Gets copied as clean text.
Upon clicking FILE->EXPORT you get an export option with which you can export the entire set of notes/annotations as RTF/RTFD/FDF or TXT.
I personally love Highlights and its ability to export to everything. If all of this is a headache to you, you could manually copy paste to evernote (but you can't export each highlight to evernote - too cumbersome, and pdf annotation is a premium feature).
Highlights and its ability to export to markdown, and most recently to @BearNotesApp format is great. It could export to evernote too. So, I'm using that now. Whatever windows alternatives you guys have, let me know! Following tweets on android.
There's this app PDF HIGHLIGHTS EXTRACTOR - works well for extracting annotations and exporting to PDF format. It's by a co called TIKSCORP.
Lithium Epub Reader - has a very nice interface, you can read highlights/annotations separately in its interface as a standalone element. You can also export the annotations as a HTML or TXT format file, which is great for most people. The formatting is damn clean. Only epubs tho
The following images show you the html formatted content from Lithium and the text format file too.
For PDFs, use the MOON+ reader. Clean interface, nice reading, separate section to check out highlights and annotations. Also can export as html/txt.
Check out the @getliner app on android that's on beta right now. Very good usability for web highlighting.
