The STK500 is a programmer for most of the Atmel AVR chips.
You write in ASM, C, BASIC and generate a HEX file (machine code) and use the STK-500 to burn the chip. I does HV parallel, Serial, etc. It also has switched and such to play on the board rather than make a breadboard.
If you are going to get into the AVRs, look at the dragon. I want to sell my STK500 and get a fragon so if I ever go back to Atmel, I will have ICSP/debug, the Inchworm/ICD2 stuff has spoiled me.