If you know how to write assembler files, the simplest method to include those ".S" files in your project is the "iard" method.
You must use the GCC assembler syntax that is a bit different from the AVR assembler syntax.
A minor problem is that the ". S" files should be placed in a subdirectory of "libraries". "\arduino-1.0.1\libraries\AssemblerFiles" for example. You can use as many assembler libraries subdirectories as you wish but must reside in "libraries" directory, not in your projects/sketches directory.
http://arduino.cc/forum/index.php/topic,37588.0.html
Note: the syntax, general estructure and philosophy of inline assembly, asm(), asm(), and so on, is a real nightmare designed by sadists computer scientists