I'm having the exact same problem, and haven't yet been able to find a solution. The freezes can happen anytime, sometimes i go days without a problem, other days it'll happen a couple of times in the same day. I can usually move the mouse, and it only lasts about 30-60 seconds before going back to normal.
I have tried all the obvious, updated drivers, disabled start up programs, disabled all non essential services, disabled power saving features on some hardware, disabled all non used hardware such as webcams, network card, internal modem(i'm on a laptop), etc. Yet i'm still getting the freezes. Its froze when i'm using internet explorer, civ 4 beyond the sword, media player, virtual dj and various other programs. I don't think its a problem with any of my software as it has happened with lots of programs. And i know its not a hardware issue, as vista worked fine on this laptop. From what i've read its a windows 7 issue, i'm just waiting for someone to find a fix, or hopefully microsoft will release a patch.