My favorite is Yesterday's Enterprise with Cause and Effect coming in a close second. Timescape (while not a pure time travel episode) ties Cause and Effect as my second favorite.
That's about where I stand as well, though sometimes, just for the entertainment factor, Cause and Effect edges out Yesterday's Enterprise.
Time's Arrow never really did much for me. I enjoyed the stuff about the beginnings of Picard and Guinan's friendship, but they could have gotten that in one episode - seems it was an excuse to do put the characters in a 1900 setting without using the holodeck again and then stretched to fill two hours.