My bike, purchased about two years ago, came with Magura Julie hydraulic brakes, which are Magura's 'entry-level' disc brake system. Even Magura indicates that they are not to be considered for either serious cross-country or downhill usage. Rather, they are mainly for "touring", whatever that means. These brakes are my only experience with bicycle disc brakes so far, so I don't have anything to compare them with. All I can say is that they ARE an improvement over the Deore cantelever brakes on my 15-year old Specialized.
My buddy has the AVID BB7 discs on his Cannondale and really likes them, and I've never read anything except great things about them. AVID rates them as a serious high-performance brake system. Seeing as I can procure all the parts from JensenUSA for less than $200 these days, would they be a significant improvement in stopping power, modulation, fade resistance, etc., over the Julias?