I built this PC about 2 months ago, and it was running nice and quiet, but I turned it off for about 4 days and when I can back and turned it on, it's suddenly loud. I see no dust buildup and it's running cool, so I'm not sure what it could be. I don't think they're running at 100% but they are running significantly more than they were before. Even changing fan settings in BIOS hasn't fixed the problem.
What fans are causing the problem? If it's the CPU fan, try resetting the BIOS by removing the CMOS battery. Also, try installing the newest drivers for your video card and motherboard. You might have missed an important driver, and the system itself might be sending incorrect temperature readings.