Well, my wife and I are going on the Brillance Panama Canal cruise on 4/6/2007. We debated long and hard whether to stay on the ship or take a shore excursion.
We book a balcony cabin, so when we are going through the locks (has to be in the morning) we can watch everything from our room, or go atop ship to see it from there. I would imagine it will require us getting up pretty early.
If you don't take an excursion, you will not be allowed off the ship until it goes back through the locks and docks at Cristobel.
So, you have to decide if you want to be a part of the journey back through the locks during the day or if you want to see more of Panama.
We decided we wanted to see more of Panama so we have already booked the train & bus tour. It will make for a long day, but, hopefully, one we will long remember.
I should say that I am a big train buff, so our decision may have a bias!
In fact, we are taking the banana plantation train the next day in Costa Rica too!