Ex bike machanic and shop manager here for various shops over the years and an avid biker...
I think you already have a very capable bike, and can be upgraded into a decent trail bike with some smart purchases. But if you are looking for a new ride, really look at what the majority of your actual riding is and base it around that. If your trails are tight twisty single track I wouldn't go with a 29'er, they are slow to respond, think of driving a '74 cadillac, great for long smooth cruising, but the 26" wheel bikes with a shorter wheels base wll be more like a honda prelude, quick, great maneuverability and quicker to stop. Both have their place where they excell, but may not be interchangeable.
Disc breaks, great invention, but not the be-all end-all. In your budget, they will likely be mechanical (cable actuated) which have come a long ways over the years. Avid are my favorites but Hayes aren't bad either. Learn to tune them your self, especially if you have lots of low intruding brush or sticks that bounce off your wheels. Nothing worse than a rubbing rotor to listen to.
As far as upgrading your current ride, if you want to explore that option, I would start with wheels/tires. Go as light as you can afford, Stans No-Tubes is worth it, and ask the LBS regulars what their tire of choice is for your area trails. Next would be brakes, upgrading your cable housing has an amazing effect as well as the V-brakes themselves. My race bike (single speed) has vintage Avid Ti V-brake rear with a custom arch support and has crushed cheap rims. I have an Avid BB7 disc front, so mixed is still good if proper components are chosen to balance the brake power. Once you get better on the trails (sorry for assuming your a noob, but your questions kinda hint at it) I would consider upgrading the fork. Many factors including frame geometry and your weight, riding style, trails, brake and wheel combination come into play when choosing a new fork. Thankfully each factor narrows it down greatly, so you may be left with only a few from each major manufacterer to choose from.
So to recap, consider how you ride, where you ride, what you want and what your budget can handle. About the bike you posted, looks to be a fairly standard package option, baseline components on a nicer frame. Trek is a great brand (thanks Lance...) but other companies to look at that can give great performance for a better price I would consider Iron horse, GT, Fuji, and even some Mongoose.
Happy Trails!
-Xander