sudo su -
apt-get install avrdude
avrdude -F -v -v -v -v -pm168 -cstk500v1 -P/dev/ttyUSB0 -b19200 -D -Uflash:r:program.bin:r
should do the trick then

Ubuntu has the following packages =>
avr-libc (1:1.4.7-1) [universe]
Standard C library for Atmel AVR development
avra (1.2.2-1) [universe]
Assembler for Atmel AVR microcontrollers
avrdude (5.5-1) [universe]
software for programming Atmel AVR microcontrollers
avrdude-doc (5.5-1) [universe]
documentation for avrdude
avrp (1.0beta3-6) [universe]
Programmer for Atmel AVR microcontrollers
avrprog (0.2.1-14) [universe]
Programmer for Atmel AVR microcontrollers
The full list is here
http://packages.ubuntu.com/hardy/allpackages