I’ve probably purchased 300 books in the last year for research purposes, not to mention all the fiction my wife gets (and so do I, if it costs $3 or less). For the newer ones , buying them as eBooks is generally an option. But the state of software, DRM, and copy protection for Kindle books is a mess. Kindle’s software (like iBooks) is deliberately crippled – no copying into another document, no printing, and especially no way to copy diagrams. I’m running Kindle’s software on my Mac and on an iPad, rather than using a Kindle tablet, but that barely helps.
The best solution (on a Mac) seems to be using Calibre to convert Kindle books into ePub, or into a PDF. Then select ebook reader software on the Mac, and another on the iPad. (Marvin seems to be the best on the iPad.) But I find that I often end up with 3 or 4 copies of the same book floating around in different locations and formats, such as:
- PDF in my research database
- The original Kindle book, in my wife’s Amazon account (since we share an account to avoid paying twice for the same novel)
- In my Calibre database on my Mac in ePub
- On Dropbox in ePub
Keeping my highlights and notes synchronized among them is a disaster. I’m very tempted to convert everything to PDF, since I have good PDF reading and management tools, but then I lose the additional features of a book format.
In an Amazon forum, someone wrote that there is no right to print a Kindle book, just as buying a hardback does not give any rights to the paperback version of the same book. My response:
This is partly a myth, vigorously perpetuated by publishers. Consumers DO have rights in the law, including “fair use.” Printing out an entire book is generally not legal, but if it’s purely for backup purposes it might be. (AFAIK there is no case law on this, in other words, nobody is sure exactly where the limits are.) Printing small parts of a book is certainly legal, such as by doing a screen print.
Some publishers, such as O’Reilly, sell DRM-free books and give liberal rights to use them in different ways. However if you buy their books through Kindle, the software does not allow it. (You can then go to O’Reilly and for $5 they will sell you a DRM-free version.)
All in all, the situation is a mess. The best practical solution is generally to not use Kindle software (or tablets) to read Amazon books.
Art and Science in Technology - Roger Bohn's Blog 
What if you want to compare content in two different books? Kindle is inconvenient, isn’t it?
You are absolutely right. All e-books are inconvenient for comparisons. I admit that I was not even thinking about physical books, which continue to have various advantages over e-books. One of them is being able to line up a bunch of books side by side. Another is that it’s faster/clearer to flip between post-its in a physical book, and to skim-read, than the analog with an e-book.
Of the hundreds of books I’ve bought for my flying project, 95% are physical. First, many of them are old and don’t have e-books at all. Second, a used physical book is usually less than $5 including shipping. Kindle versions are generally slightly below the price of a new paperback book, so they are more expensive. Third, the drawbacks of working with e-books, especially for casual reading.
By the way, I’ve long thought that many drawbacks of e-books and other electronic media are partly due to limited screen real-estate. Lining up material on an empty physical disk gives a lot more “screen space” than a 21 inch monitor. Not to mention that I work 99% of the time with a 15 inch Macbook, which is smaller still.