We have already discussed some missing Precolumbian sites on the list, a subject close to my heart. They are abundant in many countries like Peru, Ecuador, Chile, Panama, Costa Rica, Puerto Rico, Belize and Guatemala.
An unknown fact is that Brazil too has some such interesting sites, which unlike sites in the countries I have just cited are mostly unknown. Brazil has the tendency to ignore its Precolumbian past openly assuming that the gatherer-hunters society which predated European domination were primitive and left no significant traces.
The only Precolumbian site on Brazilian list is Cerra da Capivara. On the T list there are none.

I would like to suggest three important sites:

1) Kuhikugu - http://en.wikipedia.org/wiki/Kuhikugu
The only Precolumbian urban site in the Amzonian forest. It presents an independent development unique in the Americas.

2) Itacoaitara do Inga - http://en.wikipedia.org/wiki/Ing%C3%A1_Stone
The only site in South America with a Precolumbian writing system, so far undeciphered.

3) Calcoene Megalithic Observatory - http://en.wikipedia.org/wiki/Amazon_Stonehenge
The only Precolumbian astronomical site in South America.

BBC4 recently had an interesting program called "Untouched Amazon" which, inter alia, looked at the "myth" of lack of significant human impact on the Amazonian ecosystem during pre-columbian times.
In particular it looked at the Geoglyphs of Acre province. This is the BBC link with pictures of a geoglyph (if they keep it on) - though even if its download time wasn't about to finish you would probably be unable to see it from outside UK!
http://www.bbc.co.uk/programmes/b0122njp

Herewith some other links to said Geoglyphs
http://media.theworld.org/images/pdf/amazongeoglyphs.pdf
http://www.megalithic.co.uk/article.php?sid=24435
Given the location one wonders about contact between the jungle/mountain and desert peoples of South America