Thaiphoon Burne is the most popular and probably the only tool for modifying the spd.bin. It has many built-in templates and you only need to select the speed, clocking, and voltage you like (e.g., DDR3-1688/DDR3-1333 and CL10/CL11 and 1.35V/1.5V) and it will do all the rest calculations and generate the spd.bin for you. Then, the only thing you need to do is to flash the spd.bin to the spd chip on the ram, and reboot, and your ram stick is overclocked.

Unfortunately, it is only available on Windows. So I have one harddisk loaded with Windows 7 and Thaiphoon Burne specialized for this work.

I haven't found any linux software can do this unless you calculate and modify the spd.bin by hand. (If anyone found one let me know)