Could be your graphic driver. Try opening Wordpad and open a big document. See if that jerks as well. If so then it is probably a graphics setting. Try changing resolution to see if that fixes it. Also check to see if your processor is maxxed out. Could be a nasty running in the background.
Does sound like a nasty. If you aren't viewing the net, is there any network activity? I would recommend downloading Adaware and/or Spybot and checking. Failing that, try downloading Firefox and see if that works better than IE.
What sort of spec machine are you using? Ive found dodgy flash animations can really choke machines four years old (PIII 700 or so) and even noticably slow new machines. If your always viewing a particular site, or have it open in another window thats a likely culprit.
PIII 700 should be able to handle most stuff, but I've found that even my G4 1.2Ghz starts juddering on badly coded javascript ads, like the Hotmail ones you get on some forums these days.