I am living with this issue for a long time now. The freezes did not occur before updating to 11.04. Since the update the following happens:
All running applications do not respond for about 11-2 minutes. Meanwhile I can move the mouse and switch tasks with Alt+Tab but clicks or other inputs have no effect. If I listen to my HDD it makes "reading" noises in a rhytmic way with a frequency of about 1 "noise" per second.
My first guess, a broken hdd, did not hold because I testet it on Windows and nothing the like happened. An update of Ubuntu is not an option because my Partition is too small, plus all Ubuntu updates decreased performance in the past.
Happy to hear about hints and tips (: