I'm using Ubuntu and every couple minutes it goes unresponsive for a half second to a full second, which isn't normally a problem but makes trying to code extremely frustrating when your trying to hit backspace or navigate the code and nothing is happening. The problem is, the freezes are so brief that top doesn't have time to show me what is spiking the CPU (assuming something is, but I don't know what else could cause this).

Does anyone know how to troubleshoot this performance issue?

Edit: I've tried login in with Gnome Classic (No Effects) instead of Unity but it still freezes up every once in awhile.

Edit: The CPU graph doesn't seem to be showing any actual spikes so it seems you were right and my original diagnosis of CPU spikes being the problem was incorrect, I now suspect IO wait. I don't recall this happening for the brief few weeks I had Windows 7 Starter running on it though, which leads me to believe it isn't (just?) the hardware.. is there anything I can tweak to improve this? I'm using an Acer Aspire One D257, with Ubuntu 11.10.

Edit: Output of dmesg is at http://paste.ubuntu.com/1060054/ and kern.log is at http://paste.ubuntu.com/1060055/