I think that the best method was the one chosen by bruce eckel for "thinking in C++". It's just a HTML document.
It's good because a book is supposed to be read, as webpages, and after all, i already have opera running all day, so, no more apps are needed for that. One problem is that if the page is too big, poor opera crashes (ie doesn't, though), and there's no way to make bookmarks (to specific parts of the webpage) or to underline stuff. Still, i think it's better than chm and pdf because the search is fantastic and, as long as you have a good browser, the letters are perfect for reading.
Another advantage is that it only takes a mouse gesture to switch between reading the book and checking new posts at DC