Well, in MY opinion, handwritten thank you cards (like the nice ones you can buy in packs from a Hallmark store) look professional while being both thoughtful and personal at the same time. You at least had to take the time to go to the store, buy the cards, and write out each one, instead of just copying and pasting the name of a program into a generic form letter that you mail out everywhere.
But that's just my opinion. If you want to send something, either is fine. I can't imagine that there's any program out there that has a column in their applicant ranking database for handwritten vs typed thank yous.