There are alot of 'favorite passages' that make for good reading. In addition to those that you and Ken mentioned, I like students to see the siege passage in War 5: 258-302, partially because it has the funny "son is coming" האבן באה ('patriarchal' is specifically Hebrew, not Aramaic) and also War 6: 281-310 where the strange occurrences before the fall of the temple and the sad prophet are described.
If students are mainly interested in NT, then things like the Archelaus delegation to Rome as the background of the parable in Luke 19 are also good reading.
If touring the Land of Israel, then the fall of Yotfat, a nice walk above the real Cana, is excellent though quite long. (Seems it was important to Josephus
Other passages of interest would be the description of Gamla (a short movie is available at the museum in Qatsrin) not too far from Gamla itself,
and the description of the sea battle on the Kinneret is good when going to see the Galilee boat at Ginosar. Lowering soldiers down the Arbel cliffs makes a nice read//hike, too.
We've thought that a special Josephus course would be nice to run, where texts are read/discussed and sites visited, but the amount of text that students would need to read are so extensive that enrollment would be limited and not financially feasible.
The same limitation applies to doing a course on Herodotus or Thucydides. But the battle of Salamis overlooking the island makes a nice read after a Greek breakfast on a clear day. And then there's Pausanius.
I can only see this as feasible in a "pinnacle program" (to be discussed at the ETS Applied Linguistics section, Baltimore 2013) where third-fourth year students have reached a level of classroom fluency on par with what vigorous French/German programs achieve at upper division.