I know you'll hear other opinions as well, but here's what I did on my '00 281SC...
Cobra, Bullitt, Mach 13" Fronts and
Cobra, Bullitt, Mach 12" Rears. They gave a small (~5%) discount when purchasing both together, and I came in right at the $800 mark shipped... That includes hi-quality rotors and 4 new calipers. I was able to sell my stock stuff to a Fox-body guy piecing together a 5-lug upgrade.
It's pretty "complete" - I needed 4 extra copper washers for the rear hose/caliper connection (you re-use your rear hoses), 3 qts of 75W-140, silicone, and a couple bottles of brake fluid. Worst part of the job is that you need to pull the rear axles to install the new rear brackets. It's all Ford parts, so no worries down the road about finding replacement stuff. I went with plain rotors and plain black Mach I calipers. You have several choices of calipers - black Mach, black "COBRA", red "COBRA", or red Bullitts with the running ponies. For a few bucks more you can bling it up with drilled &/or slotted rotors as well.
Some people will say the rear isn't as necessary as the front. I was due for complete brakes anyway, and the larger vented rears are a decent upgrade from the small unvented stockers. Helps visually fill the wheel a little better as well. The combo I went with looks "stock" - just "bigger".
Another option would be Baer's front "Track" setup (
$655 + free shipping - PN 4261007), and if you have a few bucks extra, their rear Eradispeed +1 setup (
$229 shipped - PN 2262011), which re-uses your rear calipers and doesn't require pulling the axles. That gives 13" rotors all around... Some will argue the front/rear balance is upset by that... Others say it works great...
Here's mine: