Logos Bible Software is my program of choice for both devotional reading of the Bible and studying. One of the main reasons is actually simple: it offers easy annotation of text. You don’t have to worry about keeping track of your notes or only using certain highlighting colors because it offers a full array of note-taking tools, including highlighting, changing the font color, underlining with different styles, putting various brackets or boxes around words, drawing arrows in the margins, placing various symbols around words, and many more. In fact, their software and many books are available for free (most of the books and resources aren’t, however).
This Christmas season, they are holding a sweepstakes for their newest version and it includes just about every book you could ever want for Bible study and it comes with a MacBook Pro laptop. Although they normally offer extremely reduced prices for their digital books anyway, they claim that there are about $100,000 worth of books in this package (if you were to buy them at a bookstore in print).
If you are interested, you can enter once per person per email address per household.