Wow, still trying to digest this. Microsoft has 90+% of the very important desktop OS market, and a huge chunk of the enterprise market, yet they're of less value than a boutique brand.
This is a two sided story, I think. For one, Microsoft has become a shell of a company. They have had a handful of new initiatives over the past decade or two, but they've failed to execute on any of them. (Edit: duh, Xbox. They nailed that one.) Most of what we've seen is rebranding of existing product lines and incremental updates.
Apple, on the other hand, should never have gotten this big doing what they do. This isn't entirely a technology story, this is a business management story. They kept their margins viable. While the rest of the world raced towards zero profit margin in pursuit of volume (sure we're making a tenth of what we used to, but we're selling twice as many!) Apple kept their margins sane. They've had the rest of the pieces in place too-- tech, design, cachet, MS backlash-- but keeping their profit per unit such that they didn't need to slit their own throats meant a lot.
For those going on about P/E ratios like they're some sort of fudge factor that the market uses to push their pro-Apple conspiracy: give it up. This is what the market values Apple at. They anticipate that Apple has more room to grow that Microsoft, or HP or whomever. Apple is at about 21 or a bit less. MS and HP are at 13. This simply means that investors expect Apple earnings to grow faster than the other two. Given the number of business changing product releases Apple has had recently, versus the number from the other two, I don't think that's an unreasonable expectation.
Apple will continue to fluctuate up and down. The relative rankings are sure to change once the economy comes out of eclipse. The point here isn't whether Apple makes it to becoming the most valuable company in the US, or holds on to number 2-- it's that they have undoubtedly become a force to be reckoned with. This has to be one of the great turn around stories in corporate history.