Hipmunk seems to basically just be an attempt to mimic ITA's graphical UI with the ability to purchase tickets, which seems like a dubious business proposition (we'll see). I would think Orbitz could easily just stop doing its affiliate program with them, and then quickly enough make its own identical layout...

And matrix.itasoftware.com is indeed awesome-the query language lets you do incredibly useful stuff you cant to anywhere else. The hard part is then twisting the arm of orbitz/travelocity/etc to get you to book the exact same flights.