Fly between Panama and Colombia. Copa Airlines in Panama and Avianca in Colombia fly between Panama City and major Colombian cities including Cartagena, Bogota and Medellin. This is the most comfortable, quickest, and possibly the cheapest option. Direct flights between Panama City and Cartagena take just over an hour, and between Panama City and Bogota 1 hour 30 minutes.
Wait for a private yacht. It is possible to hitch a ride on a private yacht travelling between Panama and Colombia. You will have to wait around for a suitable boat, pay your way and help out on board. A good place to start looking is the yacht club in Colon, Panama. Alternatively, try message boards in hostels in Portobelo, and Cartagnea in Colombia. The calmest conditions, and therefore busiest time for yachts, is March to May.
Jump from boat to boat. This is a complicated but cheap route. First, take a bus from Panama City to Miramar. Once there, you will need to allow a day to travel by boat past the San Blas Islands to Puerto Obaldia near the Colombian border. In Puerto Obaldia, you can get your exit stamp in your passport and find a lancha (fast boat) to take you around the Darien Gap to the Colombian town of Capurgana. From Capurgana, regular passenger boats travel to Turbo; a major town on the Pan-American highway. From Turbo there is easy access to the rest of Colombia. Like all options involving small boats, this route gets much more difficult when the seas are rough between November and April. If travelling from Colombia, just do the route in reverse.
Take a tour through the San Blas Islands. Many small boats offer trips between Panama and Colombia including three days visiting the San Blas Islands. These islands lie along the Caribbean coast of Panama and are worth a visit in themselves; no wonder then that these combinations of tour and transit are popular with backpackers. Boats start in the Panamanian towns of Porvenir or Carti and sail to Capurgana or even on to Cartagena in Colombia. In the San Blas Islands, sea conditions are clam but once in the open sea you can expect to have a rocky voyage. Sea conditions on the trip from Colombia north tend to be calmer. Hostels in Panama City and Cartagena are good places to find out more about the various boats.
