Because of How to read a book I decided to make notes and marks about everything I'm going to read (speaking about educative literature).
It's also because I unfortunately realized that I do remember nothing from my previous reading I'd need to.
In How to read a book there is very brief information about that - some software and techniques.
Unfortunately for me I haven't found any usable solution. Why? The best format for making notes is still a paper book. But since a lot of material I read is usually in electronic form and printing doesn't seems as a suitable and economic variant, I had to find another solution.
I have also books (books is kind of """zavadejici""" - I'm using this term as all reading - articles, blog posts...) in several different formats - EPUB, MOBI, PDF, HTML (fetched from websites) etc. To handle these I use Calibre. Of course, some of the books I luckily have in paper form, but it is minority.
I also use several different devices for reading: Amazon Kindle 4 with Duokan firmware, laptop and in necessity also my smartphone Samsung Galaxy SII.
It's currently impossible (of course, as far I know) to manage all books in various formats in sync with all higlights, comments and notes.
To solve format dilema I decided to convert all files to PDF, since it's currently the most keep same format I know (besides DJVU) and there are a lot of utilities which can work with PDF for notes and can convert to it.
I search for several free note taking software for Linux where I mainly looked for possibility to export PDF with notes. I'd found two choices: KDE Okular and Xournal. There is big difference between these two - since Okular is whole PDF viewer with all it's features, Xournal is simple and stupid (in a good way) note taking software for PDF.
Another difference is the size - if you want to use Okular, you'll need to install all KDE dependencies, what in my case means about 50 packages which I DONT WANT (I like KISS). Xournal needs about 3 additional packages...
I've found out that Xournal is really just to much stupid to my needs. Okular is great, but as I said, I don't want 50 other packages in my PC. Besides that, Okular don't know how to export pop-up annotations which makes it unusable.
Even if you've found good software for annotating, it wouldn't solve one problem - reference manager. You would still need to use some other reference manager to keep your bibliotheque in good shape.
The least bad - Mendeley
So my choice is Mendeley. It supports only PDF, but as I stated, there isn't other more suitable format for me and this is first compromise I made with Mendeley.
Mendeley is quite good with annotating PDFs and can exports them along PDF (how to export them to other formats here). All in all I'm quite satisfied.
I hate one thing about it - every time it is run (or when it sync database) it creates
~/Documents - I don't use this folder and I hate when SW make what it wants with my delicate folder structure... I solved that by running this through script, which delete this folder when I close it. I also don't like that it isn't really open source.
I'm using t for short time, but will update my experiences.