Setting aside my type nerd instincts and just addressing the UX implications of the choice:
Verdana was designed as a screen font, and so is very well hinted at small pixel sizes on 96 DPI screens. It also has an extremely high x-height, which improves its readability especially at small sizes. It is infinitely more legible for screen use than Arial.
Arial is fundamentally a bastardisation of Helvetica, which was designed in 1957 for print and signage. That Microsoft have done a good job hinting the font makes it a passable display font as well, but it will never be as useful for that use as Verdana is (and its cousins Tahoma and Georgia are).
All that is becoming far less important going forward though, with the invention of ClearType (on Windows) and Quartz text rendering (on OS X), and especially as we begin interacting with websites nowadays on devices like the iPhone 4 with extremely high-density displays, all of which are attempting to make type on-screen more like type on the page.
Which is all a really roundabout way of saying "it's more of a visual design and branding question than a purely UX consideration".