Folks will jump all over me for saying this but this is my advice regarding Colon.
Do not try to go on an excursion on your own. The immediate port area and adjacent shopping center is safe, however the rest of the city of Colon and the surrounding countryside is not safe for independent travel.
Panama is a beautiful country with 500 years of history, 100 years of canal history, and generally wonderful people to see and visit. There are enough political and criminal problems to not venture out on your own. The major tours offered off the ship are escorted by police working directly for the Government tourist office. This gets the buses through traffic, protects the passengers, and protects the buses and your belongings while you are off the bus.
Panama is one place where I would definately recommend a ships tour or just staying
within the boundaries of the new port area.