Via Rattle's Abusable Technology meme:

Let's say that you're a dangerous Canadian terrorist,
] bearing the clearly suspicious name "Guy Lafleur". Now,
] the American government is aware of your activities and
] puts you on the CAPPS blacklist to stop you from boarding
] the plane. Further, let's assume that you're too
] incompetent to get a fake ID.... You have someone who's
] not on the blacklist buy you a ticket under an innocuous
] assumed name, say "Babe Ruth". This is perfectly
] legitimate and quite easy to do.... Then, the day before
] the flight you go onto the web and get your boarding
] pass. You print out two copies, one with your real name
] and one with the innocuous fake name. Remember, it's just
] a web page, so it's easy to modify. When you go to the
] airport, you show the security agent your "Guy Lafleur"
] boarding pass and your real ID. He verifies that they
] match but doesn't check the watchlist, because his only
] job is to verify that you have a valid-looking boarding
] pass and that it matches your ID. Then, when you go to
] board the plane, you give the gate agent your real
] boarding pass. Since they don't check ID, you can just
] walk onboard.

Links to possible solutions.

How To Bypass Airline Blacklist Without Much Effort