I prefer Hydraulic. Make sure that they are pre-bled. Also, if you remove your front tire, be sure and not engage the brake. Can cause some issues on some brakes. I like Hayes, and Juicy. Hope this helps.
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Always depends on what your plans... Mechanical brakes have many issues with rotors, however moving to hydraulic requires some training: little touch and your bike stops. Personally I don't like Hayes. Got leaks many times with 9. Avid juicy are very good. My XC includes juicy 7, but the best one are "Hope". In any case buy additional pads for long trips. Also ask your local bike mechanic :-) They always have some opinion...
I agree with the hydraulic posts. I used Hayes 9's for about 4 years now with zero maintenance. I now have Shimano Hone hydraulics for the new bike and they are fine.
I did consider mechanical for one application that is unique to roadie. A cyclocross or road bike with top brake levers can't work with hydraulic. I haven't built the roadie bike yet because of the mounts for the brake caliper, but I'm looking into it. If I do put rotors on a roadie, I will continue to use the top bar brakes that I modify all my roadies to and the cable is the only way that this will work.
For MTB, hydraulic seems to be the best. Avid Juicy, Hayes, Shimano seem to be fine.
6 inch rotors for XC bikes. 8 inch rotors for Trail, All Mountain, DH bikes.