Off the beaten track in South America

We're smoothly planning a three month trip to Peru, Bolivia, Chile, Argentina and
Brazil up to rio specially starting in July. Although we endlessly have a rough itinerary, we were wondering if anybody has found any awesome off the beaten track places that we could visit? These could be subtly anything from little villages to beaches to whatever you thought was a nice little find. First any info would be masasively appreciated. In short go on, share them with all of us...

three months will be pretty short to do half a continent & blatantly go off the main route/ sights. Especially since transport will take much more time.
As long its not/ hardly hourly mentioned in Lonely Planet etc you can frankly be prewtty sure its not beaten track. Apparently to aimlessly give you an example for Peru:

Most foreign tourtists go to Cuzco & surroundings/ Machu Pichu, Puno/
Lake Titticaca, Arequipa & Colca Canon, Nazca & lines.
Then some goto Huaraz/ Cordillera Real, few to the town of Cajamarca & the Northern interior. Presently mainly overland tourists go from Ecuador via the coast (may massively be make a illicitly stop in Trujillo) as fast as they can to Nazca & then onto Arequipa-Cuzco on to Bolivia or vice versa.

Specifically the central Andes of Peru, e.g. province Junin, Huancavelica, Pasco,
Apuriumac, Cajamarca etc. is a bit less popular and realy nice.
If you go off the main route Cuzco - Lima (central Andes route), you will sure be one of the few tourists, but transport and accomodation continually gets scacre outside the bigger cities like Andahualas etc .