I will soon be releasing a number of free bitstreams to mine with FPGA's with better ROI's than GPU's, and if you want silent mining you can use the Nexys Video card (XC7A200T FPGA). Be warned, you can only mine Keccak (Smartcash, Maxcoin) and SHA-224 (Bismuth) profitably, but the card draws minimal power, needs no fan, costs $490, and makes around $2.11 per day at today's prices which is more than many GPU's.
What miner are you using with your FPGA? How many watts does it use?
Nexys video ($490) burns around 15W, makes around $2 per day; Avnet KU040 ($975) board burns around 30W, makes $7-$18/day, Xilinx VCU1525 & Bittware XUPP3R ($3995-$5895) burn 80-175W and make $25-$120 per day depending on the algorithm. I programmed the FPGA's myself and forked an open source CPUMiner build and adapted it to communicate with the FPGA's. I'm planning on releasing the bitstreams in around 4-6 weeks.