I've just programmed a spare key I bought off ebay. Very important that you buy a key that has the same chip. I had the key copied at a local lock smith first. Then followed these steps. This is only for the 2003 to 2006 4runner models. Sorry, I don't have info on any others.

1. insert the master key (black) into and out of the ignition 5 times leaving the master key in the ignition.
2. open and close the driver's door 6 times.
3. pulled the master key from the ignition. Security light stays on
4. inserted the spare key and waited for the security light to quit flashing. about one minute. Key has been programmed
5. inserted the master key and started vehicle to exit the programming mode.
6. shut off vehicle and inserted copied key. Started vehicle.

I just wanted to share this with folks and maybe help you save about a hundred bucks.