Getting around Uganda requires patience and a sense of humor. The road network is improving, but once you leave the main highways, expect red-dirt roads with serious potholes. That said, the country is compact and the transport system works -- it just works on African time.
Matatus and minibuses. Shared minibuses (matatus) are the backbone of Ugandan transport. They connect every town and are cheap -- Kampala to Jinja costs about 10,000 UGX (under $3). They leave when full, not on a schedule, and they are always packed. The main departure point in Kampala is the chaotic old taxi park in the city center. It is an experience in itself.
Boda-bodas. Motorcycle taxis are everywhere and are the fastest way to get around in cities and towns. They weave through traffic that would stop any car. Agree on a price before you get on, insist on a helmet (they should have one for you), and hold on. Boda-bodas are cheap and convenient but they are also the most dangerous form of transport in Uganda. Use them for short hops, not long distances.
Buses. For intercity travel, full-size buses are more comfortable and safer than matatus. Link Bus, Gateway, and YY Coaches run services between major towns. The Kampala to Kabale route (gateway to Bwindi) takes 6-8 hours. Kampala to Gulu in the north is about 5-6 hours. Post Bus, operated by the post office, is slow but reliable and departs on time.
Special hire. A "special hire" is a private taxi -- you hire the whole car. This is the most comfortable way to travel and essential for reaching remote national parks. Your hotel or lodge can arrange one, or you can negotiate directly with drivers. A full day's hire costs $50-100 depending on distance. For safari trips, a 4WD with driver is the way to go.
Domestic flights. Aerolink and Fly Uganda operate small charter flights between Entebbe and airstrips near major national parks -- Bwindi, Murchison Falls, Kidepo Valley, Queen Elizabeth. They are expensive ($150-350 one way) but save you 6-10 hours of driving on rough roads. Worth it if time is short.
Driving yourself. You can rent a car in Kampala or Entebbe, and it gives you total freedom. A 4WD is essential for the national parks. Driving is on the left. Roads between major cities are decent; roads to the parks range from okay to terrible. Fuel is available in towns but can be scarce in remote areas -- fill up whenever you can.