As we had limited time and wanted to maximize our time, as well as ensure we had someone familiar with conditions, we got quotes from 4 travel agencies based in Mali; we selected Papillon Reizen, which is run by a Dutch lady and her Malian (Dogon native) partner, and is based on Segou. The price quotes were all pretty similar, but we selected Papillon in large part due to the wealth of information they provided, as well as their ability to meet our main goals while in Mali, in the relatively short timeframe available. (several other agencies suggested more abbreviated schedules, and seemed uncertain whether we could reach Dogon country and return within our timeframe)
Our tour went well, and in spite of worries about possible issues or threats to our safety (such as the attacks last year in Sevare and Bamako, among other places), we felt safe in the areas of Mali which we visited. And very welcomed - the Malian people are very warm, and would often even ask us to take their photos (without asking for payment in most such cases; most, especially the kids, seemed to really enjoy seeing their photo on our digital camera displays afterward). We especially liked Dogon country - very scenic and cultural, and we wished we had more time to hike it.
We also enjoyed some short board rides on the Niger, in Mopti and in Segou, and really appreciated the mud architecture in the area and of course, the massive mud mosque in Djenne. And the varied village architecture along our routes was also interesting to see.
Overall we really had a good time and would recommend the areas of Mali we visited; of course, any visitor to Mali should always pay attention to changing conditions, assess one's own tolerance for risks, etc, but overall we felt comfortable and would like to return.
Finally, we felt that a lot of our enjoyment of Mali was due to the excellent service provided by Papillon, and would heartily recommend their agency. If their link is permitted for reference, it is http://www.papillonreizen.com
And a final note - Mali was the last nation in the world I had not visited. I was particularly touched when the head of Papillon had a Bogolan (traditional mud cloth) banner made for me to commemorate the occasion - this was a very warm gesture and a good symbol of just how wonderful we felt their service was.