Krt-jub
There are 3 airlines serving this route at the moment: Marsland Aviation (with the TUs), Sudan Air with a tired 737 and Air West, also a 737 usually. Tried them all - I wouldn't recommend any of them particularly but there aren't many other options (barge...or UNMIS plane, but difficult to get on this). Cost is about 45,000SD one way. Recommended to buy one way so that you don't get stuck with your chosen carrier coming back if they cancel, have problems, go out of business etc. Flights down from Khartoum are quite full, so you need to book quite far ahead or else push your way on at Khartoum airport. Return from Juba is usually more open.