With Lion, the three-fingered flip now launches Mission Control, so navigating through Mail messages has changed to a FOUR-fingered flip. It took me a while to figure it out on the Magic Trackpad -- it seems to call for a little practice.
A flip Up/Left brings you to the next message up the list; a flip Down/Right brings you to the next message down.
[crarko adds: This is starting to take on the feel of learning to play a new musical instrument, which is not all bad, and possibly intentional on Apple's part.]

