For me, the highlight of the trip to Timbuktu was touring the mosque. Many other mosques, like the one in the tourist center of Mopti, do not allow non-Muslims to enter, but Timbuktu was different. If you find yourself there, you will most certainly be afforded the opportunity.
Aside from the mosque, the artisan's market was interesting (as was the "regular" market). There is also the ethnological museum, which houses a few interesting artifacts from Timbuktu's past.
Unfortunately, there isn't much else to recommend about Timbuktu, aside from being a place for a hot meal and a shower upon return from the Sahara. It's a fairly dirty town (even by African standards), and even though the pressure from potential "guides" isn't what you'd experience in Mopti, it's still present unless your current guide is there to shoo them away.
Quick Tips:
If you arrive in January (around the time of the Festival au Desert), you actually will have trouble finding accommodation. Reservations will actually be necessary, believe it or not. I met numerous people who had to sleep in the homes of their guide's friends because hotels had no vacancy, not even on the roof.
Best Way To Get Around:
Use a car. Walking is doable, but be VERY CAREFUL, because Timbuktu has a large amount of open "drainage" ditches from houses. You will be spending a lot of time dodging fluids if you walk a lot in residential areas.
Be advised that as of 2004/2005, the UN has forbidden after-dark road travel with tourists in this region of Mali due to banditry concerns. Do not make concrete plans that depend on you moving on from Timbuktu after dark, as the police will likely turn you back (it happened to friends of mine, and our guide had to "bail" their guide out before they could continue back to Mopti).