The best thing I've found to keep up computer drive speeds is to partition the disk into OS and data. The system files are kept on a small partition (like 64 GB on my MBP) that's close to the inside of the spinning disk, and the rest of the hard drive is used for user data. The idea is to keep the number of writes into the OS partition as small as possible, and just do stuff on the data side so you don't fragment the OS side, and the OS side gets the fastest portion of the disk. So far it's worked out well, and when I installed Win7 on another laptop, I used the same organization which will hopefully work out fine.
Both OS X and Windows will initially put all the user directories on the system disk, but they're easy to move over to the data partition, and you can link to them with UNIX links on OS X, and shortcuts on Win7. This way, it's also trivial to reinstall the OS from scratch because you can easily backup your data separately.
This site goes into more detail: http://macperformanceguide.com/Mac-BootDriveDogma.html
It's Mac-centric, but much of what he says applies to Windows, too.