I spent time travelling throughout West Africa, and travelled extensively in Togo, Burkina Faso, Mali, Benin and Ghana. Going to Timbuktu was one of the most memorable experiences of my time there.
There are two ways to get to Timbuktu - boat or four wheel drive. From Mopti (a dirty, horrible little town full of people wating to take advantage of tourists to point of harassment) I got the boat there - a 'pirogue' - and a four wheel drive back.
Me and my friends stowed aboard a local businessman's pirogue, a very long wooden boat primarily used to transport goods but also people along the river Niger. We made a deal with him to let us sleep on sacks of grain, alongside local people, on the journey upriver to Timbuktu.
The journey took three days, during which time we played a lot of cards but also saw some amazing sights, travelling through enormous lakes and seeing local riverside villages and ports. It was really the journey of a lifetime and unlike any other I've ever done.
The food was of course terrible (rice and meat stew-not good for veggies like me-cooked on a boat by seemingly the worst cook in the world), and we ate with our hands, but seeing the local Muslim people praying to Allah at various times of the day, according to where the boat was and with such dedication, made it all worth it.
It was almost sad to leave the boat and wade ashore when we arrived at Timbuktu. Here I must be clear - some local people will try to charge you, as a tourist, a tax for helping you get ashore, a tax for entering Timbuktu, a tax for this and a tax for that. Argue your case and stand your ground and hopefully (as happened in our case) some local peopl came to our defence and we won over the sly shifty 4WD driver, who drove us from the port to Timbuktu itself.
Timbuktu is quite far from the port so don't be alarmed if it takes a while to get there. Once in Timbuktu, it's really not that big and hence there is not much to see. But the best thing to do is just wander round and soak up the atmosphere.
Beware the markets, which harbour mean men who wish to rip you off selling you jewellery etc-try to buy from nice old men instead, even if the price is slightly more. Such conniving men will also offer to show you round the town but in fact just show you their wares at their house in an effort to rip you off even more.
Get someone to take you out to stand on the edge of the Sahara desert. Sand is swallowing up the town and I'm sure in a few years it might not exist at all, so go there while you can. It is a magical place. Some houses look like those of the sand people seen in Star Wars, whilst others are more like wattle and daub. Everything is of course covered in sand , including the local bread, which I don't recommend as a gourmet delight, more as unique experience!
Accommodation in Timbuktu is really expensive so we didn't even stay the night - there is even a very out of place Hyatt hotel there!
On organising 4WD transport back, hard bargaining is required and it seems impossible to avoid paying too much. Try to share vehicles where you can with anyone you can find, that'll make it cheaper.
Our 4WD back to Mopti was plagued by breakdowns and a driver who refused to used headlights in the pitchblack when driving in areas with no roads at all. We even endedup sleeping by the side of the road because he had had enough of it all and wanted a rest. A local person also seemed to get a free ride out of us by tagging along from the very start...but it's all part of the experience.
When all is said and done it was a once in a lifetime trip that i cannot recommend more - so just do it!!!!!