Panama City [1], not surprisingly, is the country’s transportation hub. It has its major international and domestic airports, its biggest bus terminal, its main ship ports, and plenty of rental car companies.
Most travelers come to and leave the country through Tocumen International Airport, 25 kilometers east of Panama City. The nearest cruise-ship port is at the end of the Calzada de Amador [2], which is near the Pacific entrance to the Panama Canal [3] a few kilometers from downtown.
The national bus terminal, for international and domestic long-distance buses, is the Gran Terminal de Transportes in Albrook. It’s quite close to Panama City’s domestic airport, Aeropuerto Marcos A. Gelabert, also in Albrook.
Note that no roads or ferry service currently link Panama and Colombia; only airlines provide regular passenger service between the two countries.
Links:
[1] http://www.moon.com/destinations/panama/panama-city
[2] http://www.moon.com/destinations/panama/panama-canal/the-former-canal-zone/sights/amador-causeway
[3] http://www.moon.com/destinations/panama/panama-canal