Our one experience taking cats through the WTMDs
In 2005 we moved from SAN to PDX; we have three cats. I would not put them in cargo, but one option was available -AS allows up to 5 animals in cabin on a flight. So we recruited a friend (who is also owned by a cat) and paid for his ticket, and all three of us took at cat as our underseat "personal item."
However, we also started planning for this a few weeks in advance. I grabbed a row of three at the back of the plane in case anyone had allergies and needed to be moved up front (and yes, that happened). And the most important piece, I actually got the TSA involved early. We were flying weekly back and forth between SAN and PDX getting things together, and the week before us and the furry creatures made the move, while flying out of SAN, I asked one of the TSA reps what we should do about the cats. The rep grabbed her supervisor, and he told us to come early, and he would put us and the cats in a seperate room with a closed door, and x-ray each carrier indivudually.
The day of the move came, our vet advised us *not* to sedate the cats, we checked in early and made our way to the WTMDs. I told the first TSA agent what the supervisor told us to do, and she had it down. She grabbed a partner, and the two of them put is in the room where they do the private screenings. They had our friend go through the WTMD first and wait on the other side; then we took one cat out of the carrier at a time, the carrier was x-rayed by one agent with the other agent watching to make sure that only the the cat went back in to its original carrier. Since the room was quiet, the cats didn't make much of a fuss. Once they were done, the cats were brought out to our friend, and then we went through the WTMDs.
The AS agent was great and pre-boarded us along with a couple of UMs who happened to be in the row in front of us. We told the kids which cat was under their seat, and every so often, one of the kids would dive down to say hi. Everything else on board was fine, except that Samson (who has since gone over the rainbow bridge) decided that he wanted to talk for a while, and once he realized that we weren't going to take him out of the carrier, eventually quieted down.