
Mountain Bike Disc Brakes are very dependable brakes and work better than rim brakes. If you want better, more consistent brake performance in all conditions and don't really care if it weighs a little more or costs a little more, choose disc brakes over rim brakes. Disc brakes have been around for a long time in cars but weren't seriously used on bikes until the mid to late 90's.
There were definitely some issues with some of the earlier models but the disc brakes of today, cable actuated or hydraulic, perform quite well. The performance of disc brakes is considerably better than rim brakes. Especially in wet or muddy conditions. Disc brakes usually require less force to apply and aren't effected by rim/wheel condition.
The biggest downside to disc brakes is the added weight. By the time you add everything in, including front and rear brakes and the added weight of the disc specific hubs, you end up with around 150 to 350 grams additional weight to the whole bike. This weight number greatly depends on the wheels, rims, hubs, and disc brake system you choose.