What a fun article!
I HATE noise coming from my box. Part of it is because I do a bit of audio editing on the side, and the other part is because I feel like that constant humm (no matter how quiet) is just going to drive me batty one of these days. Sadly, for my setup silence is not an option because my rig is 1 part AV editing rig, 1 part game rig, and 1 part home file server, which means big parts and HDDs which invariably make noise. So for me it has been a combination of using large aftermarket coolers, low RPM fans, adding noise dampening material to the sides of the computer case, putting that case inside a noise dampened server rack, and then putting the rack some 15' away. Thankfully the server rack was free (a company I work with was going to scrap it) so the whole project wasn't terribly expensive (all told ~$200 for all coolers, fans, material and looong cables), but now I have a nearly silent computer, but with no performance compromises, and I couldn't be happier.
I think the equipment we are going to see in ~2 generations (2-4 years) will finally have low enough power requirements that there will finally be some very nice passively cooled options on the market, or (like the article pointed out) systems that have a single fan that only powers up when you are gaming or are having a particularly hot day.