By taxi
The best way to get around Kampala and the neighbouring towns is by using minibus-type taxis called "taxi". This is the most efficient and cost-effective method of transportation in urban areas, but try not to get ripped off by the conductors as they sometimes try to overcharge tourists. They usually take 14 passengers plus a conductor, though in smaller country towns overcrowding still occurs. Minibus taxis are relatively cheap, frequent in Kampala, and may make lots of stops along the way.
They run along fixed routes, picking up and dropping off people anywhere along the route. If you want to get on, stand at the side of the road and wave your arm. To get off, say "stage" and the driver will pull over and let you off at the next boda boda waiting area. You can also just say "Driver, please pull over at X". They're not marked with destinations unless you are at the central taxi parks, so you'll have to listen to the destinations that the drivers are yelling out the window. If you're not sure where to catch a taxi going to your destination especially at Kampala's two taxi parks, which are huge!, just ask a nearby driver or conductor, and they'll probably be able to point you in the right direction.
Private taxis - those which you can hire for yourself only, are called special hire taxis, and are available in most every decent sized town. Fares are negotiable over long distances as there are no meters.
By car
The roads in Uganda are comparable to many in Sub-Saharan Africa. Most of the main roads are metalled though the condition of them can deteriorate in patches. Some become extremely pot holed. Many of the minor roads and side roads are made of hard packed earth murum and, when graded, are quite quick and reasonable. However, they will deteriorate in heavy rains and wash boarding frequently occurs. The best way to deal with the wash boarding is not to slow down, but to find a speed sympathetic to the road surface and effectively skip from ridge to ridge. Untarred roads, if wet, may be impassable in the mountainous regions of the south-west. Commercial drivers of buses and trucks compound the danger, as do pedestrians, livestock, cyclists, dogs and the odd police roadblock. Plan on 60km/hr as a typical rate of travel speed will vary, though!. The best advice is drive cautiously and stay totally alert.
When planning a journey, it is best not to ask how far it is but to ask how long it will take. Local drivers normally have a good idea of how long journeys will take.
Expect to pay a lot to hire a vehicle. A sensible choice is to hire a 4x4 with a driver given that you will need local language assistance and expertise should something happen on the roads. Most places have accommodation and meals for drivers as this is common among travellers. This will cost upwards of USD100.00 per day not including fuel with the cheapest vehicles typically having no windows, a canvas roof, an assembly date in the 1970s and so on. You get what you pay for. A cheap option is likely to leave you stranded somewhere remote and that can mean days of your itinerary lost. Unless you are comfortable paying cash in advance without a signed contract and no network to help you get out of a breakdown, go to one of the major agencies.
By bus
Uganda has a decent bus system. There are two classes of buses. The "taxis" also called "matatus" are actually minibuses or commuter vans, which run fixed routes see below.
There are also real buses which run less frequently, usually leaving Kampala early in the morning. There are many companies which almost all leave from the same general area. The buses fill up, so if you get on mid-trip, you'll be spending some time standing or sitting in the aisle before somebody gets off and you can get a seat.
Both buses and taxis run along most roads between cities, paved sealed or dirt.
Domestic bus travel is reasonable and cheap between major centres, and is a good choice for backpackers with time, but may not run reliably on schedule. A trip from Kampala to Masindi takes about 4 hours and costs approximately 8,000 Uganda shillings.
Note that both buses and "taxis" do not run on fixed schedules; rather, they leave their terminal stop when they are completely full. On heavily-travelled routes, they fill up within minutes and this is not a problem, but on less-travelled routes or if getting on a large bus, be prepared to wait a while before departure.