If I have to pick only one, it will be this one:

From North to South
On the Pan American (1N) turn towards the mountains at Santa
After about 60kms at Chuquicara turn left over the river. No sign, but road goes to Ancos.
After another 20 or so kms turn right and follow the road that winds up the mountain to Ancos.
About 5 or less kms turn right on a single lane track that goes towards Santarosa and Llapo. From here it is extremely spectacular with single lane trafic and steep cliffs all the way. Go all the way to Llapo to check out the friendly town, then backtrak about 5kms to a turn-off to your left (S08-32.938' and W078-02.670') and take that turn-off. The road winds incredeble and we stayed in 1st and 2nd gear most of the time. Like I said, single lane, shear verticle dropps and no railings. After some time you'll reach the toan of Yupon, they have a hostal in town where we slept.
From Yupon follow the road towards Corongo. About 5kms before town you'll get to a T junction, turn right here towards La Pampa, another nice mountain town (petrol available at the supermarket) Another 10kms or so you get another T junction, turn right again. This road has the most incredable mountain scenery with amazing colours and good surface.
After you drop down the winding mountain pass you'll come to another T junction (S08-41.978' and W077-57.622') at the 'main' road from Santa to Huallanca. Turn left towards Huallanca, another nice, cheap mountain town. After Hualanca you'll go through the amazing Canon Del Pato, a single lane (stil) dirt track that follows this very narrow canyon on an old railway line through 36 or so tunnels. It is spactacular.
The route as discribed above took us 2 full days (250kms) and was the best ride of my life. We rode slowly to admire the stunning scenery and stoped a lot to take awsome photos. The little mountain towns are very friendly and 'unspoiled' by other tourists. The road surface was challenging (we were two up on a 1150GS) and we had lots of mud, but that just added to the Adventure. There were also very little trafic, so it was safe.
You'll need a good map to locate these towns, as they are very much off the mail drag. To re-cap in brief:
Santa - Chuquicara - Ancos - Santa Rosa - Llapo - Yupon - Corongo - La Pampa - Hullanca
I've uploaded two videos of this road here
YouTube - Peru 1 and
YouTube - Peru 2 if you like to see it.
Johan