This is a really useful and important process for reading, and I too have been frustrated by the lack of a good ability to take notes while reading in an e-book on my phone/tablet.
It's ironic, because on my Kindle (2.0) there's a built-in keyboard, which I can put notes anywhere in the text, and open all my comments in a single text file as a separate document, with hotlinks to the selected text in the e-book! So this is a solution, but, it's not on my Android phone...
One thing I have tried (and I won't say it's not a cumbersome process) is, in FB Reader, you can make "bookmarks" of highlighted text, which are very easy to return to.
Then, you can take those bookmarked text passages, and "share" them with any app - which I then share as simple txt files in my basic notepad app, "Fast Note".
After you have shared the passage from FB Reader as a text file in FastNote, you are free to add text as you like - make your comments right there in the same text file. Then, save the entire file.
You can then make a separate folder in FastNote - the title of the book, for example - and move the passage-and commented text file to that folder, to keep things organized.
This way, you would have the actual text passage, together with your comments, in an easy to read-and-access format. The only problem would be, it wouldn't be hot-linked directly to the e-book itself - you'd have to open the e-book seperately if you wanted to see the surrounding text's context, for example. But, by bookmarking the identical passages in the e-book reader, you could easily go to that passage in the text quickly.
It's a two-app solution, granted, but it DOES accomplish the desired goal.
It would be tremendous if FB Reader would seamlessly integrate a note-taking app into their reader, the same way they have done with their dictionary app (the somewhat lackluster Color Dict, I must say, though...). I'm really surprised they haven't implemented something this simple in all the years they have been producing their otherwise excellent reader.
