brakes

Alex, Saint brakes are already good and the new model will be excellent. Hope isn't for everyone and probably suit bike tech geeks better. They are reliable but do require careful set up and attention. I'd steer clear of Hayes even though the higher end models are good. Remember that your HFX Mags are an entry level and OEM product, not top shelf and the design is rather old.
Avid make good brakes. Juicy aren't for downhill though. That's what Codes are for. All Avids are reliable and work to their design brief. Also it's their own brand pads that are the best which is unusual. I don't even use Hope pads in the Hope brakes I like so much.
Curiously a very good brake is the latest incarnation of Shimano XT. I believe you'd get them for both ends for just a bit over $400 and even better is that I believe they have a six bolt rotor option so a new set of hubs is not required. XT breaks a lot of rules for a product promoted as an all mountain group with some guys saving a shed load of weight using this groupset and going freeriding, jumping etc.
As for Little Ditty's comments about the Fuel and Trance rear end looking the same, I think he was meaning from a fabrication viewpoint. I'm sure Ditty is well aware of the differences between the APB from Trek and and the twin link Maestro isolated triangle design from Giant. At least I hope he does...