I've read and heard a lot about this issue but have no first hand experience. From what I understand TSA can and does make exceptions for certain things, one of which is liquid sustaining life. If you can prove the liquid is sustaining life they can/will allow it through within reason. For instance its very obvious that water in a bag is vital to the life of the clownfish within in. BUT, how do you prove that saltwater is vital to a small coral frag that looks like a plain old rock? My friend had an idea to drop a few tigriopus pods in a specimen cup with a coral frag. Tigriopus pods swim freely in the water column so they're obviously alive...thus the water they're in is vital to sustaining life. I wanted to test this on a recent trip with some GSP and pods in an 8oz specimen cup but I managed to leave the GSP on my coffee table when I left. BUT, I did prove that GSP will be fine in a specimen cup for 3 days ;)
I've heard of several people carrying fish and other animals on the plane. In every instance the person notified the TSA agents immediately upon arrival at the security checkpoint and after some questioning they were granted access. Of course it would suck to buy that $500 chalice frag you've been looking for only to have it seized by TSA but I think with some tact and common sense you could safely transport a few frags on board the plane :)