We did the trip from UK (via Spain) to Timbuktu in 2005. Our itinerary is shown at:
On the way out we went to the end of the Route de l'espoir at Nema and then 3 days off road via Nampala (photos on website: NOMADINTENT
). (Others travel further north from Nema along Lac Fabuguine but I believe that is rather sandy and hard work on a bike; also further into the "danger zone").
The return route from Timbuktu was via Douentza, then asphalt all the way to Bamako; now it is asphalt all the way from Bamako back to Europe.
We found Timbuktu something of an anti-climax, but it was worth it to see all the stuff along the way, particularly the Pays Dogon.
If you are interested, there is a link to my photo book of the journey on the website, but if you want some more practical advice, get Chris Scott's Sahara Overland
Have a great trip.