Flipping to the index or table of contents, keeping a pen or finger in another page and flipping back and forth. Once that is figured out I will be a complete convert and stop preferring physical books.
What would be nice would be gestures. Maybe tap once, make a gesture and it remembers that gesture as a bookmark to that location. Later, make a line and the same gesture and it heads to that bookmark.
This way you can be looking at a chart, tap and make a number one. Head a few pages or another chapter down, tap and make a number two, a line and number one to look at the chart again and a line and a number two to head back where you were. Or maybe a standard "back" gesture.
Pressing multiple buttons and following many links is nowhere near friendly enough.
The gestures suggestion above still only works if you know you're going to be returning to a location when you get to it. Flipping through the book to quickly find a past location is a harder problem to solve.
iBooks has an 'overview' mode that sort of works if the book is well marked up. However it's not nearly as good as flipping, & the processor needs to be much faster.
http://ipadwatcher.com/wp-content/uploads/2010/08/ibooks-pdf...
Look at the features: a) It smells better b) You can store them and it only takes an entire room of your house c) They weigh enough such that you can curve your children's distressingly straight spines with them.