On the company the effect is like being assimilated into the Borg, but for users of their software it's like having a friend with a malignant brain tumor. You're going to have to say "goodbye" soon to an object of your affection.
I'm talking about the affect that Microsoft has on software when they purchase the company that makes it. Two cases that come to mind are PowerPoint and VirtualPC. Now there's another candidate, iView MediaPro. iView announced yesterday the assimilation. Maybe iView will be an exception. They have made remarkably great software for a decade or so. I love what they do.
Being remarkable is important to a business. Make sure your business is on the right side of the "remarkable" scale.