Good advice from Wamphryi.
As far as the partitioning goes, there are ways to "shorstroke" your hard drive to acheive better performance, unfortunately its not that great and usually not worth the hassle. I have friends that partition the hell outta their drives for various reasons, but faster usually isn't one of them. And with this comes the inherent headaches mentioned above.
Here's a few tips:
Even after a fresh install, defrag. This will help keep your drive tidy and organized. Don't forget to defrag again after loading software. It will become disorganized as you install stuff.
If operating with multiple drives, move your system cache to a drive that isn't the system drive. Depending on how much ram you have, this isn't the issue it once was with people running 1 or 2 gigs of ram. But still, if you move the system cache to another drive, the system drive won't be pinged by this activity when trying to do other things.
If using a SATA drive, ensure you are running in AHCI mode. This is something many people miss during install. It will be slower running in legacy IDE mode. You MUST be in AHCI mode prior to installing windows, after if you try to use this mode you'll hang at the windows logon window and never get into windows.
Finally, start saving for an SSD. It really does make a difference in overall system responsiveness (not just loading windows). The best bang for buck currently is in the 120GB range, I like the OCZ Vertex 2 and Crucial C300 for SATA II. Good price/performance/real estate ratio and under $2 per gig.