I started using Ubuntu 10 after I couldn't be arsed with the hassle of reinstalling Windows then the raft of things you need to just to get the OS the way you like it. Ubuntu package manager is the way that software should be installed. I have seen zero slowdown after using this Ubuntu install for 2 years.
I'm finally getting round to rebuilding my machine and I'll have to get a Windows install again just to play games natively. I may dual boot. But I digress.
Like others have said a full reinstall is the proper yet painful way to get your machine back to it's original glory. Nhasian is spot on with creating an image when you've got your basic Windows install in place. Avoids all repeating all this garbage.
You can run programs like CCleaner
to clean up the registry and other ye olde temp file clogs. Windirstat
is a nice program that will let you find where all the space is being taken up on your hard drive. Deleting unnecessary files and uninstalling programs is an obvious one.
It looks like you might be using a SSD so fragmentation is probably not an issue for you but I suppose you could point Defraggler
at that 1TB Seagate drive.