I'm with Cordelli here. It can be some program/process running amok.

The most usual culprit is Flash and Flash-based sites. I'm not an Apple fanboy, but Steve Jobs was right on Flash being more a scourge than an asset, specially on the hands of lazy programmers.

Try enabling (at least temporarily) IE's Flash-blocking feature. If your slowdown was caused by Flash, you will not experience it anymore, albeit at the cost of a less media-rich experience.

For more complete blocking, you could install .......:
http://simple-........com/

If you still suspect an infection (and before trying something more "radical"), you could try McAfee's Stinger - It's a stand alone program that contains detection for the more usual and current threats only. You would need to download the current version at:

http://us.mcafee.com/virusInfo/default.asp?id=stinger

(I'm an Avast user, not a fan of McAfee main programs, but do like Stinger for its simplicity and approach. Keep in mind that it is not a substitute for a full anti-virus program)