Is Skype running when this happens? Skype can take up a good portion of CPU resources.
Not on an i5-2500K. It have adequate resources to handle tons of applications running simultaneously.
I built my computer last month and can run games very well. However I noticed some freezing when opening programs like firefox or taking a long time to load or cant click anything on my screen for a couple of seconds.
Could the slow performance be caused by my CPU or HDD? and if it's a HDD problem, would upgrading to a Caviar black help?
If you haven't done so, upgrade your Catalyst to the latest driver (12.1). The previous versions contains fixes about lagging mouse response (which should be carried over to the latest).