Trek and Specialized make great bikes. I own a 2001 Rockhopper Comp and a 2006 Trek Fuel Ex 9 (but we've already had this discussion).

I pulled up the specs on both bikes (the Trek 6500wsd and the specialized stumpjumper disc, right?)

While the components are a bit nicer on the Specialized than the Trek, those disc brakes on the Specialized are mechanical disc, not hydralic disc breaks. Huge difference....

As long as you fit well on the Trek, I'd me more inclined to go with that bike (if you have your heart set on one of the two). It will be easier to upgrade the drivetrain components than it will be to up grade those mechanical disc brakes to hydralic (very costly, especially if you can't install them yourself & and even if you can, you still need costly tools like a torque wrench to do it).

As someone else stated, if you asked your lbs to upgrade that specialized stumpjumper to hydralic that would be a good option also. But, I'll bet it would push the price up to $2000 give or take. So it depends on your budget and how each bike fits you.

Also, Hayes Sole brakes are the bottom of the line hydralic brakes in that product line and I'm not sure how good they are. So you might want to do a little research before you buy.