Performance would dramatically increase if it was two separate hard drives, but if it's a single hard drive it doesn't matter how you partition it or where you put the data. After a HD gets filled past 50% you're going to see a dramatic speed decrease. Whether it's on your main partition or otherwise, it doesn't matter.
If you're looking to increase your speeds, get a small crappy 120gb HD (7200rpm or faster is recommended. If you can afford a 10,000rpm, get it). Put windows and all the essentials for your computer to run properly on that drive. Then use your existing drive (the one you're using now) to store everything you want. Be advised though that if you have to format the main crappy little drive for any reason, you'll have to delete the programs that are installed on the backup drive. There will be no file associations or shortcuts to your programs when you format. You can make all of the shortcuts and file associations manually, but it's a nightmare.
My recommendation would be to install the programs on the backup drive in a folder called "Program Files" and also back up all of the install exe's and make ISO backups of any and all program disks you have and put them on the backup hard drive. If you like using the default "My Documents", "My Pictures" etc folders, simply re-direct where they point to and point them to a folder on your backup hard drive.
Of course with all your data being arranged like this, you MUST have an external hard drive to back up the backup drive. If you do this you'll notice a very high speed increase. If you don't want to do this, then partitioning your HD won't make things any faster.
