even though you may have nothing open on your desktop, there are a lot of background processes going on. its a pretty easy fix, just open up task manager, go to the processes tab, and close down anything that isn't anti-virus, java or some windows process. Speeds up your comp a CRAPTON. Also, I'd try defragmenting your hard drive and cleaning up your registry. There are a few programs for the registry out there, but the defragmenting software is installed standard. Just go into start>all programs>accessories>system Tools>Disk Defragmenter. It might take a few hours to defragment, but your comp should be a bit faster. Also, make sure your comp is updated, as windows is constantly coming out with stuff to help it run faster and be more efficient. Sorry if this seems really simple to you, but i don't know you're background with computer stuff, so yeah. If you have anymore questions, ask me on skype, my username is Hikazaru37. I can also show you what to click if you do screen share, so yeah, good luck.
OH one more thing: install the optifine mod, or get spoutcraft, on spout craft i got my fps to over 1500, when i normally get about 250, so yeah.