My own experience: sit on the left side flying to Cuzco, you will see Lima right after departure and then, if you're lucky, you may even see Plaza de Armas approaching Cuzco airport. In general, you will have mountains on the left and the ocean on the right after the departure from Lima, and I suppose the mountains are much more interesting.

Here is what the Lonely Planet guidebook to Peru (the 6th edition, from 2007) says on this topic: "When flying from Cuzco to Lima, try to check in as early as possible so you can get a seat on the right-hand side of the plane for the best views of the Salkantay's 6271 m peak. Some pilots like to fly quite close to the mountain, and the views are sometimes stupendous. (Sit on the left from Lima to Cuzco). Very occasionaly a different route is taken over Machu Picchu."