Off the top of my head, it's exceedingly difficult to decide what was my favourite experience across this continent- but I'll try and name a few.
Peru
My entire time in the jungle was brilliant. From random monkey encounters, swimming daily, spending the night in the canopy and even just simple pleasures like opening and drinking a coconut straight off a tree- the jungle was, without exception, just incredible.
From there, the plane ride to Cusco set the tone of the next month- the scenery of the Sacred Valley is breath taking. The closest I can compare to it is a vast version of Scotland's glens- impossibly grand mountains that rise straight out of the river bed, set in front of a glorious backdrop of glaciers to the tune of perfect weather. Altitude is amusing to get to grips with, too.
The Nasca lines- what an experience. The nutty pilots and their tiny planes only added to what was, quite simply, damn cool.
Huacachina- perhaps as close as it comes to Paradise, I fell in love with this desert oasis and it's sandbuggying/boarding madness.
Lake Titicaca is incomprehensibly vast. More so, I got to dance in traditional Peruvian dress and the sun rising and setting, both simply beautiful- what more could you want?

Bolivia
Copacabana- not of particular merit itself, but nearly missing the boat, watching the World Cup with hot waffles and getting a hostel (with hot water!) for only 7.5 bolivs (40p!) certainly stick in the memory.
La Paz- cheap as chips. This city is diverse, and our hostel was in the heart of the witches market. Llama foetus, anyone? Eight days was barely enough to scratch the surface, but mountain biking down 64km of the world's most dangerous road, general haphazard tourism with the Ben and Dave comedy duo and attempting to bribe my way into the infamous San Pedro prison were certainly amusing.
The Road to Ururo. Not a particularly favourite memory, but it definitely stands out for quite how horrendous it was! Whilst the Bolivians are quite fond of striking, I don't blame them for hating the condition of that road. Due to the road blocks, we had to enter Uyuni on a bus (the train was blocked too) at a just plain nasty hour, book our salt flats tour in the early hours and leave again, after trying to sleep on a tiled hostel floor in front of the surreal Spanish Cartoon Network on a nearby TV. Southern Bolivia is cold- that night was certainly well below freezing.
The Saltar was incredible- vast tracts of white desert, an underground burial site and our dubious music collection blaring from the landrover. I feel particularly sorry for the Canadian guy- he lost a bet one night, and the forfeit was of course, to strip down to boxers and run about in what was near minus 20. Ouch!

Argentina is lovely
Salta is beautiful, Buenos Aires is beautiful, Argentinian steak is beautiful and the people are beautiful. Overall, a fairly consistent result for the Argentinians.
What particularly stands out: eating three hostel-cooked (yet still adorable) steaks in one sitting, not waking up until 4pm in our hostel in Buenos Aires after a night's clubbing, trying (and failing admirably) to learn the tango before watching an incredibly impressive show, the districts of San Telmo and La Plaga themselves, 
And of course, I've ran out of time. I feel it must be said, however, that Buenos Aires is without a doubt the best city I saw in South America- the one city I'd truly love to live in.