There are several ways to get to Tombouctou, and none of them is easy. Of course you can fly to the city with Air Mali, but this airline's nickname (Air Maybe) makes you think twice. The two best alternatives are the boat or the 4WD. By boat you can reach Tombouctou from Mopti, it will take about 3 days to get there. But most large pinasses have a toilet, so you'll survive.
I went there by 4WD from Mopti. The first 200km you'll drive over a good road to Douentza. The last 200km are through the desert. It is a tough ride, but this can also be fun. We were lucky it had not rained much. One week later this would have been another story. We reached the ferry to Tombouctou at 17.30. After a short ride over the dyke we reached town.
Of course, if you like adventures, it is also possible to reach Tombouctou by camel. From Marrakech (Morocco) it takes about a month, from Douentza a week. But trust me...a 4WD is better...
Before you make a trip to Tombouctou, make sure you have also arranged the trip back. Getting there is easy, but getting back is another story. The easiest way to do this is to just rent a 4WD for the whole week.
After having visited Tombouctou we left for Gao, in the east of Mali. There is no road between Tombouctou and Gao so it takes some time. We got there in two days. The drive is spectacular. You will pass high sand dunes and big plains. When you arrive in Gao you will feel like you've just driven the Paris-Dakar rally.