Its most likely a problem with the registry, i agree. I used a reg cleaner a while back without really considering the consequences. That probably killed a few necessary files. The process that causes the cpu jump is always the internet program im using. I use both IE and firefox interchangably depending on what i want to do. IE is fast, so i use it for simple tasks such as getting pictures or checking email. But ill use firefox for more complicated things because its safer. Im sure you know the process names for firefox and IE.
Usually when it happens, ill open up the task manager to see what is doing the lagging. Every time its been the internet program.