I have an ARM kit beside me and a Linux kernel source code patched with Xenomai on my machine. I understand I can send data to the kit through an USB cable and a (windows-based, of course) software, but I'm stumped as to exactly what I should be sending that would make the kit run Linux.
(clarifications from comments: It is an Atmel AT91SAM9260-EK kit. It uses SAM-BA and SAM-PROG for the loading and unloading of data through either a serial or USB cable.)
You might want to check out some cross compiler like OpenEmbedded which will help you compile the kernel for the ARM architecture.
I'd start with the ATM91SAM9 Linux software package from Atmel and follow the instructions.
Linky:
http://www.atmel.com/dyn/products/tools_card.asp?tool_id=4335
Otherwise, you need to get GCC setup with an ARM back end on a Linux box, build a Linux binary and then figure out how to load it on the devt board.
i would suggest jtag and openOCD, then you just use the JTAG to place your filesystem and kernal image in the flash memory, in a place wear our bootloader can find it. you might have to change your bootloader. another option is you might start up your micro, then insert a bootloading program into the RAM of the program then change the program counter to point at it. that bootloading program can init the UART/USB then you have a host side program that transers the files. this method is very complicated and generally only good if you don't want to spend 100$ on a jtag (hint, buy a jtag they are useful)
http://www.linux4sam.org/twiki/bin/view/Linux4SAM/SoftwareTools#SAM_BA_Linux_initiative
http://www.atmel.com/dyn/products/tools_card.asp?tool_id=3933
HTH