I have been seeing this issue since Vista. Note that I have only ever seen this on my desktop with an ATI video card. I have never seen this in a laptop with Intel video. I have seen this in Vista, 7 and now 8.1, again on my desktop only.
Anyways, I originally had an ATI HD2600Pro card. The many posts here indicate that it happens with Nvidia cards too. The ATI 2600 card runs pretty warm, so I got an ATI HD 5450 card. The performance is a little less, but it does run cooler. I still
have the issue.
The other fixes in this topic did not apply to me. I do not have Java installed here. iehighutil.exe is not on my system. The Power Options, PCI Express->Link State Power Management->Setting is already "Off".
It always seems to happen when I scroll the page in IE. I am not a game player, so the GPU is not being taxed at all. I tried changing the IE11 rendering option to "Use software rendering instead of GPU rendering", but it made no difference.
So I just applied the registry fix available here. Will see if that helps.