When you have a long series like that -- A, B, C, D, E...X, Y, Z -- X would be third from the last, Y would be second from the last (or penultimate), and Z is last (or ultimate). If these represented, say, people in a line/queue, person Y would be the second from the end or the penultimate customer. The "bottom" would work for something arranged vertically, i.e. "the third exam paper from the bottom of the stack".