If you've got Vista, you can directly upgrade to Windows 7, easy like cake. But you really shouldn't. Maximum PC's got a detailed guide to the cleanest possible Windows install for the best performance.
Overall, the guide's pretty similar to what I do every couple of years with a new Windows install to keep performance snappy. A biggie is to start with fresh hard drives—read/write speed is faster than whatever you bought two years ago, and the closer to full a drive, the worst it performs, so a bigger drives helps. I'd also check out a 10,000RPM or faster drive, if you're got cash to burn, though they were pretty cheap earlier this year.
For prep, there are a few steps that I should start following myself: Collect all of your application license keys (they recommend Magic Jelly Bean 2.0 to do the dirty work), deactivate and deauthorize apps, back up data from apps like iTunes, get your drivers together (especially video card and motherboard).
Then you just install Windows on your new hard drive (make sure you install to the right one), and once you're up and running you can copy files over from the old one. The other major pro tip is to buy a second new drive once you're all setup, and use that as a disk image and file back location, using a program like Acronis True Image. Overall, a solid, detailed guide you should check out if you're doing a new Windows installation, 'cause there's probably some tip you didn't know. BTW, here's Lifehacker's guide to building a new computer to slap it on. [Maximum PC]