Yesterday, my computer started acting sluggish. After checking the process in the Task Manager I noticed that System Idle process was hogging all of my CPU, despite having numerous apps running: photohop, firefox, xampp, a minecraft server, and eclipse. I was using the programs too. I understand that Sys Idle is running to run regardless and will run when the computer isn't doing thing but it was doing stuff. After doing a clean re-install of Windows the problem still exists. It's slowed my computer down enough to slow my computer time by about 15 minutes. I've never had this happen before. I don't know if it's a software issue or a hardware issue.
It is normal in Task Manager for the System Idle process to show a large percentage use. What it really means is that is the amount of processing power that isn't being used. So on a totally idle system System Idle would show 100%. In practice a system is never completely idle, so you'll see something like 98 or 99%. This is completely normal.
Edit: Check disk access; a sluggish system usually means that you have heavy disk acess. Is the light on almost all the time?
I tend to agree with The_Prophecy. It doesn't sound like you have excessive disk access, you have a new installation, and the System Idle thing is a red herring. Sounds like it could be a hardware fault.
Could also be faulty hardware sending excessive interrupts. You could do a partial check of that by turning off most of the built-in components (audio, serial and parallel ports, usb - if your keyboard isn't usb - and network adapter) in BIOS to see if that makes a difference. If it does, re-enable them one by one, checking again, until you find which component is causing the problem.