After some consideration, we did:

1. Jerusalem (full day).

2. Masada and Dead Sea. (Be sure to take the Masada option; the "floating in the the Dead Sea" part is a "fun once" well worth doing for the novelty but once done there's not much more to do there. And don't forget your flip-flops.)

3. Jerusalem and Bethlehem. We decided after going to Jerusalem the first time that we wanted to visit Bethlehem as well, and the only tour to there we could book included the morning in Jerusalem. As it turned out going back to Jerusalem the second time was a serendipitous treat. Some overlap/repetition of course, but the first day's tour guide was a historical scholar, and while he hit the religious high spots we also spent some time at the museum looking at the Dead Sea Scrolls. The second time, the guide was more Jerusalem architecture-oriented, and we visited the Wailing Wall and some archeological excavations in the Jewish Quarter. Really interesting to experience the different perspectives.