Unfortunately, I have found more serious problems with the Command Line book I started this thread with. It lists a LOT of commands like mkd i r. What is that? It means that they apparently didn't hire a proofreader to look at this book, or the proofreader didn't know what was up. (I speak as a former professional proofer.)
But I still like the good things about the book, and it still reminds me of a book I bought about DOS, many years ago, by Peter Norton! That is, it tells me a whole lot about Linux, some of which I don't know.
Thanks for mentioning The Trouble with Physics! Sounds like the kind of book that might interest me; I'll take a look!
At some point, perhaps I'll compile the recommendations in this thread (and other related ones, if I discover any) and make an official list. I think that such a thing is needed; I'd LOVE to see lots of well-formatted Kindle books. So far, they have been pretty dismal, not from the reading point of view, but from the attractiveness perspective.