How to vary the supply voltage for Xilinx Virtex-5 FPGA ML501, ML506, and ML510 boards?
I assume what you want to change is the FPGA core voltage, generally called VCCINT. First of all, the disclaimer: the Xilinx specs for VCCINT are fairly stringent, and while it's likely that the hardware will be okay at a lower voltage, there is no guarantee.

Let's consider the ML501 board. First we get the schematic from Xilinx's website; it's freely available. On the first page, we see that all the power stuff is on page 21. Okay, great. On page 21, we see that U24 handles the VCCINT, nominally 1.0V at 10A max. The part is a PTH08T240W.

Now we go to TI's site and pull up the datasheet for the PTH08T240W. It looks like an adjustable regulator controlled by the resistor hanging off pin 8, in this case R179. Using the equation on page 11 of the datasheet, we can use a different resistor value to set a different VCCINT.

That's the basic approach. You can check the other boards for yourself; it's entirely possible that you may find fixed regulators. In that case, you'd have to replace the entire regulator, which would be a pain.