By ship
A ferry on the Congo River operates, if security permits, from Kinshasa to Kisangani, every week or two. You can pick it up at a few stops enroute, though you have to rush as it doesn't wait. A suitable bribe to the ferry boss secures a four bunk cabin and cafeteria food. The ferry consists of 4 or so barges are tied around a central ferry, with the barges used as a floating market. As the ferry proceeds wood canoes paddled by locals appear from the surrounding jungle with local produce - vegetables, pigs, monkeys, etc - which are traded for industrial goods like medicine or clothes. You sit on the roof watching as wonderful African music booms out. Of course it is not clean, comfortable or safe. It is however one of the world's great adventures.
By Truck
As smaller vehicles are unable to negotiate what remains of the roads, a lot of travel in the Congo is done by truck. If you go to a truck park, normally near the market, you should be able to find a truck driver to take you where ever you want, conflict zones aside. You travel on top of the load with a large number of others. If you pick a truck carrying bags of something soft like peanuts it can be quite comfortable. Beer trucks are not. If the trip takes days then comfort can be vital, especially if the truck goes all night. It helps to sit along the back, as the driver will not stop just because you want the toilet. The cost has to be negotiated so ask hotel staff first and try not to pay more than twice the local rate. Sometimes the inside seat is available. Food can be bought from the driver, though they normally stop at roadside stalls every 5/6 hours. Departure time are normally at the start or end of the day, though time is very flexible. It helps to make arrangements the day before. It is best to travel with a few others. Women should never ever travel alone. Some roads have major bandit problems so check carefully before going.
At army checkpoints locals are often hassled for bribes. Foreigners are normally left alone, but prepare some kind of bribe just in case. By the middle of the afternoon the soldiers can be drunk so be very careful and very polite. Never lose your temper.