Well theres fan out there with a controller that can be installed on an expansion slot. Like the Silverstone that I have has a controller but I used another 5 and 1/4 controller for it though. Or he can he can do some mod and install it on the sides.
the fm121 mentioned is excellent, and coupled with a Zalman fanmate2 it can help quiet things down. I got one with my cpns7000-cu and didn't think to use it (since mobo has cool-and-quiet) until I built my media player, and I am using it to control the 80mm intake fan at the lowest setting - near silence... I just zip-tied it to my mobo header cable bundle so it didn't rattle around.