The announcement of the new iPhone 3GS is expected today as part of the Apple Worldwide Developer's Conference opening address. Several other new Apple products could be unveiled as well, so it should be no surprise that the Apple Store is down right now.
There are a lot of different reasons for the Apple Store to go down, but when you consider the proximity of this occurrence with the WWDC, it sounds more than a little coincidental. It's probably safe to take this at a sign that something is going to be released during the conference today, even if Apple decides to sit on the new iPhone 3GS a while longer.
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The developer's conference starts in just about a half hour, so we should know more very shortly.