Briefly, about 45 miles of the Canal. Most Panama R/T's only do what is called a "partial transit" and some do not even do that; they just dock at Colon 2000 which is near downtown Colon.
Having said all that, let me backtrack a little and add that I think I remember reading recently that at least one cruise goes all the way through the Canal, turns around in the Pacific, and then goes back through (I may be totally wrong on this!!!).
As I said in the first sentence, most R/T's do a partial transit, which means that the ship goes through the first set of locks that are located near the Atlantic, pass into Lake Gutan, anchor, let passengers with prebooked tours disembark, and then later sail back through the same set of locks and then docks at Cristobal Pier (an industrial port area in the Canal Zone).
The problem with a partial transit is that unless you do a land/Canal tour of somekind you are only going to see about 5 miles of the 50 mile Canal.
We have done all three of the major cruise trips; 1) full transit, 2) just dock at Colon 2000, and 3) partial transit. The full transit was by far the best. However, full transits usually require much more of your time and money so those two things become the real limiting factors IMO.
Just a word of caution, becareful when booking a Panama Cruise, the cruise lines are very good at poorly wording exactly what their ship will do in Panama. I have seen many, many, very confused people (based on their posts) on this board and others about Panama Cruises.