Microsoft has taken a hit from the younger generation where I generally see a lot of contempt for them. Many companies are using Linux on their server systems. This is business that Microsoft could have had if companies didn't look for something that would take them partially outside of Microsoft's grip.
The monopolistic practices have come back to bite Microsoft in that it made them complacent with their products and they are paying a competitive price for that now in major product slips. The complacency can certainly be seen in the myriad security problems that they've had to spend a lot of engineering time on.
And monopolistic practices were unearthed. Something that those in the business knew about but really couldn't do much about.
One other place where it's been hurt is the reputation and the perceived attitude of Gates and Ballmer. Some CEOs can pull of a good show on the stand but a lot of them wind up looking like total fools against a professional prosecutor.