Are those the only 2 bikes you are considering? For the price of the Stumpjumper HT disc (1300) you could pick up a 2004 Ironhorse MKIII by mail order. Check Supergo, Randall Scott Cycles, etc.
You can just about afford a new full suspension bike for the same price you are looking at for either of the bikes you mentioned....not to mention Ebay.
If you are constrained by whatever reason to buy either of the bikes you mentioned, I would compare the frame geometries....I think the cannondale is a bit more relaxed which will give a better downhill stability, while the stumpjumper will be a steeper angled bike meant more for the racer.
As far as the shocks go, i would much prefer anything Fox over the headshock. You will be forced to stick with the headshock in the future, whereas with the Stumpy you can switch to any standard steerer tube size fork.
Both are great bikes, but you should consider all of your options as well.