Bear in mind that the CPU usages are averaged across all processor cores but most programs do not make efficient use of all cores. For instance if you have a dual core processor and you are running an intensive application that is doing most of its processing in one thread, the application's process will not tend to show more than 50% CPU usage. In this case the System Idle process will be around 50% and this is normal.
If you are having serious problems there are lots of things you could try:
Check for viruses, rootkits etc. using a decent security software suite.
Check system performance settings: right click on My Computer and choose Properties. Click the Advanced tab then click the Settings button in the performance section. The Advanced tab has a number of options including processor scheduling. The options are normally set to give priority to programs rather than services.
Run a disk check on your hard drive(s). It is also worth checking the drives(s) S.M.A.R.T data using a program like Everest Ultimate since a failing drive can cause the kind of symptoms you've mentioned. I know because I have experienced it myself.
Try disabling any non critical programs running in the background (e.g. virus scanners) to see if it makes a difference
