I agree with this: O’Reilly’s books look great on the iPad. I just bought a couple from oreilly.com (they’re 2-for-1 right now with code “BYEBK”), and I’m impressed with their approach. Each book is DRM-free, and you can download it in PDF, mobi and ePub formats (the latter of which works in iBooks on the iPad), or you can install it into Ibis Reader.
For comparison, I tried a Kindle version of another technical book (from a different publisher) and I was very disappointed. Important formatting elements from the print version were not preserved, such as using a different font to differentiate code samples from descriptive text. Formatting and layout isn’t such a big deal for novels, but they’re downright imperative for reference books. O’Reilly’s Kindle editions do preserve formatting, but even still, either their own ePub editions are nicer, or iBooks just does a much better job than the Kindle app for iPad.
Compare how the same page looks in iBooks vs Kindle for iPad: