I've put together some Makefiles and the Arduino framework to make it easy for you to compile and upload your Arduino projects without the IDE (which is java and annoying for some people).
The story behind ArduinoPure is... Firstly, I wanted to be able to compile and upload my Arduino programs just like I am used to with my AVR projects, by using a Makefile (which contains avr-gcc and avrdude stuff). Secondly, I wasn't able to get the Arduino IDE fully working with my STK500 (it always replaced the programmer setting for some reason... maybe a bug?) Additionally, the Makefiles I found online were outdated and didn't work for me.
ArduinoPure solves all those problems. I even included a Makefile to compile with the STK500 to an ATmega8 (Makefile.stk500_atmega8), which works perfect for me. Basically, with the right configuration, you can put Arduino programs on any MCU using any programmer you want.
Oh, feel free to fork my repository and add Makefiles for your own setups (different programmers/arduino boards/MCUs). I will happily accept pull requests.
And here it is: GitHub - omnidan/ArduinoPure: This is a project to achieve compiling programs for the Arduino without any external programs like the Arduino IDE. It uses all the standard programs you love so much: make, cc, ... This is also the only way I was able to flash arduino programs to microcontrollers with the stk500. (of course, open-source ;))
(I've also put ArduinoPure in the playground wiki under the Others section, I hope this is okay.)
EDIT: First post here, yay 
I'm usually not such a social person, which is why I didn't post anything here yet. Please don't judge me by my amount of posts.