out of those countries, I've only been to Peru (3.5 weeks). I also drove extensively in Peru, from Lima to Cuzco to Lake Titicaca and back.
first recommendation - don't drive in Peru if you can help it.
Lima - I wouldn't spend much time there at all. huge city, full of pick-pocketers. if you spend time there, don't walk around with anything expensive. I drove in Lima, and it's an adventure. I don't recommend it.
I completely agree that flying to Cusco from Lima is the best way to go, followed by tours/modes of travel where locals drive. We drove, and had tons of trouble with our ittshay rental vehicles. the rental car agency also added an additional $10,000US (no lie) to our rental bill after we had flown back to Canada. had we not taken pictures of the vehicles before and after we rented them, showing that they were left in excellent condition, we would have had to pay the scamming bastards. we were also shaken down by police 3 times on the road - twice we had to pay them off or risk losing our vehicles or be arrested, once we were forced to scatter/flee an extremely corrupt officer. not fun, but Peru isn't Canada.
Paracas - the water is cold, but the beaches and sand dunes are really cool to see. we did some sand boarding, swimming, and there are a few neat archeological sites nearby. I'd only do this if you are driving from Lima to Cuzco, but it's worth the stop if you drive down the coast.
Cuzco - awesome city. lots to do, but (as YvanF said) white people pay several times more than locals. negotiate everything, and don't be afraid to walk away. we spent 4 days there, and wish that we had spent more time.
Nazca lines - highly recommend if you have time. we chartered a plane for $100US/person, it's the best/only way to truly see them. several of our group had Montezuma's revenge, which did not work very well with riding in a small Cesna, with no air flow, doing loop-de-loops. you've been warned haha.
Machu Picchu - if there is one thing in Peru that you see, this is it. we initially planned to hike the Inca trail, but heavy rains were the end of that idea. the train was comfortable, and we took a bus up to the Sun Gate. for $5, the bus from the bottom is well worth it as there's a lot of elevation and only takes 10 minutes. up to you. be sure to climb the Huana Picchu spire, as the views of Machu Picchu from there are fantastic!
Lake Titicaca - pretty neat place. if you go there charter a boat out to the floating islands. we didn't stay on them, but wished that we had.
my last recommendation - don't drive in Peru!
