A very good introduction into SPI programming is at SparkFun. A popular one seems to be the USBTiny ISP from Adafruit. To program a chip, you will need a special programmer which reads commands from USB to drive the SPI lines to program the chip. It's also called 3-wire sometimes because it uses three wires to communicate. SPI stands for Serial Peripheral Interface and is a way for microcontrollers to communicate with each other or with the outside world. ATMEGA microcontrollers like the one in the arduino that are coming straight from the factory can only be programmed using the SPI or JTAG interface.
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