If cpu usage isnt at or near 100% when you have this freeze then i would suspect the video card and then the ram or power supply. But you have already replaced the vid card.
On the other hand i hate to seem to contradict Bill as he has likely forgotten more than i know, lol.
Bill has listed:
marginal power supply
leaking capacitors
intermittent contact at keyboard/mouse port, whether PS/2 or USB
bad or failing network adapter
You can check for leaking caps fairly easily and get that out of the way, you will see leakage or the top will not be flat, it will be round and then look at the bottom, it may be separated from the motherboard.
That out of the way, its also quick and easy to check the ram by using google and downloading memtest86 and check your ram, one stick at a time.
And its quick and easy to swap out the keyboard and mouse to see if thats the problem.
The power supply, if you have another, swap that out.
If not then you can go to techrepublic and sign in as its a good tech source anyway and they have a great manual on how to troubleshoot a power supply, or you can use google to find another. You do need a multimeter, preferrably digital but i am told an analog will work as well and they are cheap to buy!
Still, in my mind, there is that nagging suspicion of malware\virus at work.
So i would make sure my antivirus is up to date and run that, then some combination of adaware, spybot search and destroy, stinger (Macafee) and there are many more. The ones i mentioned are free and you can google them. I think you do need to make sure its not a bug of some sort, but thats only my opinion.
Good advice + great people = tek-tips