I have a query :D, acording to the theory, the dc-dc converter are noisy, and i've just checked reference design for FPGA of Altera and Xilinx, They use dc-dc converter, but how we can avoid the noise, capacitor coupling is enough??
There are different kinds of DC/DC converters out there, like linear and switching. Linear a real quiet, but typically pretty low current. Switchers can deliver more current, but generate more noise. It depends on your requirements. There are also some pretty low noise switchers out there, like TI's (formally National) Simple Switchers, I think those can get you anywhere from 1A - 10A. I've used them in a past design with an A2GX, they worked out well, and are pretty easy to use. There are similar products from Linear (uModules), Intersil, etc. The datasheets will give you the typical noise output.
Altera development kits are good examples of sufficient power supply filtering. Typically, switched mode DC/DC converters have input and output filters to avoid distribution of the switching noise. Bypass capacitors at all power supply pins, that are required by the FPGAs in any case further reduce supply ripple. Finally, sensitive PLL or transceiver analog power supply nets get additional filtering.