You can get Xcode for 10.3.9, but you might need to install it from your original 10.3 CD's.
Once you have Xcode installed, and you've downloaded and extracted the avrdude-5.4-arduino-src.tgz file, you just need to open a Terminal (in Applications > Utilities), change to the right directory (e.g. cd ~/Desktop/avrdude-5.4-arduino), then type:
This will check out your system and configure the rest of the process accordingly. Then type:
If all goes well, this will create the avrdude binary and avrdude.conf file. It will probably give you an error about yacc or flex, though. In that case, you need to install bison. Just download it from the GNU site, and do the same thing to install it: extract it, open the terminal, cd to the directory, run ./configure, run make - then run "sudo make install" to install it (you'll have to enter your password). Then try doing a make in the avrdude-5.4-arduino directory again.