Could you please give some more information about your PC (e.g. specs)
Anyway, it looks to me as a simple memory issue. I used to have the same issue, when many programs (talking about 1/2 programs) were open and I open up another program the PC stutters and you get a bad input lagg from your mouse and this soon finishes. This bumps up your CPU usage high causing the problem, strictly to optimize RAM usage (as it runs out of RAM) which leads to the issue. am I right? Or it could be continuous.
Basic issue, how much RAM do you have? And what OS are you running? Try seizing on some background applications otherwise my best bet would be to get some additional ram. If you have 1GB of RAM it is far too low for modern applications holding in mind there are many background processes as well.
Hope this gave you some insight.