More simply, I'll add to Siempre Viajando's 5 good suggestions:

1. use a taxi who just dropped off a pax, avoid standing taxis
2. ignore drivers who aggressively honk at you
3. use older drivers
4. assess the driver while negotiating (takes some practice)
5. walk away from any ridiculously low fare (takes some knowledge)
6. taxi with a cage to protect driver is a positive
7. use the trunk
8. lock the doors
9. leave windows down a bit to make smashing more difficult
10. sit behind the driver
11. call (or fake a call) telling your friend the taxi number
12. listen in to his cell calls, or better, tell him it is prohibited from using a cell phone while driving

I am not disagreeing with the recommendation a first timer should just simply take a Taxi Green, you should. In fact, do not take just any Green Taxi driver pestering you – go to the Taxi Green counter and get logged in and driver recorded, tariff paid.

I am disagreeing with the general tone of the dangers of taxis to and from LIM in this thread, it is not as bad as some suggest. I have taken taxis to and from the airport over 100 times (or more) this past year and not yet kidnapped or robbed... except if I had used Taxi Green who charge me twice the rate I normally pay. I use taxis almost daily in Lima, and, like Siempre Viajando, never had a problem. Except once I broke one of his suggestions (didn't negatiate fare ahead) and had a quite heated discussion with the driver after - but I know how to argue in Peruvian.