AVR Studio  is the official Atmel programmer.  It interfaces with the STK500 and AVRISP via the serial port.  It's also an assembler editor and compiler.

PonyProg is a serial device programmer software with a user friendly GUI framework available for Windows95, 98, 2000 & NT and Intel Linux. Its purpose is reading and writing every serial device. At the moment it supports I²C Bus, Microwire, SPI eeprom, the Atmel AVR and Microchip PIC micro.  It interfaces with an STK200/300 compatible parallel port cable/adapter (no longer supported by Atmel)

UISP is the GCC command line programmer (Linux only I believe)  It's part of the GCC distribution and uses an STK200/300 cable

All are free

Imagecraft C, CodeVision C both have programmer software that can talk to the AVRISP, STK500 and STK200/300 adapters so no additional programmer is needed.