If you're looking for a TOTALLY silent computer, "think outside the box." literally. For me I can accomplish this quite easily, I just turn my stereo system up and VOILA, no computer noise. However, if you're going to be serious about this, look to the car manufacturers. Believe it or not they have made completely silent cars. The trick is not to eliminate the noise producers, it's to eliminate the sound waves.
I wish I could remember all the physics behind it, but I can give you the basics. Sound travels in waves. You only hear the sound at the peaks of the sound wave. Either called nodes or antinodes, I don't remember. The trick to silence is a computer controlled machine that produces a sound that creates the exact opposite sound wave. When the two collide they cancel each other out, the peaks become flat (or very close to it) and therefore you hear no sound.
This idea was scrapped by car companies for safety reasons (imagine not being able to hear an oncoming car's horn, rumble strips, weird engine noises etc...) but it is used in other industries where noise is a factor. Large machining companies have used them to elimnate danger to workers' ears and for an all around better work environment. While these are large scale machines a smaller scale most likely exists. Take for example the automobile industry. These things can't be TOO expensive, car manufacturers don't put things in that cost them too much money, and space in a car is somewhat limited, which means they can't be huge. I'll look around and see what I can find about such a machine.