I keep meaning to mention this in a context where Hipmunk people might see it.
One little piece of design advice I'd give you based on the reaction of every single person I've shown the site to (which is in the tens at this point), is that, initially, the display for layovers is unclear.
A flight with a single layover looks like three flights because it is three separate blocks. I think you could fix this by extending the color of the boxes on either side into the connection box region. As that may not be at all clear, I've mocked up what this might look like: http://dl.dropbox.com/u/144762/Screen%20shot%202010-12-22%20...
I think it makes it more obvious what's a flight and what's a layover. Just a thought.