Update 12/22/10:
iOS 4.2 has added a “triple-click home button” feature with accessibility options, so now it’s possible to set white/black mode by going to “General Settings -> Accessibility -> Triple-click Home” and choosing the “White/Black” option. Once done, you can switch the iPhone to inverted colors at any time by hitting the home button three times in quick succession.
I still consider this a “hack”, as it turns your entire phone into inverted color mode. I would still prefer iBooks to have a true white text on black background like the Kindle and Stanza apps do.