The BIOS (Basic Input/Output System)
The BIOS is stored in a small chip on your motherboard and runs every time you turn on your PC. The BIOS controls a whole host of hardware features in your system which means that if set incorrectly, or sub-optimally, then your going to have inferior performance regardless of anything you change in your operating systems settings.
To change your BIOS settings you will have to press a key when your system starts to boot. This is usually DEL but on some systems you have to press F1. If your unsure check your motherboards manual.
Here is a handly link to a large list of BIOS settings, what they do and how to set them.
Definitive BIOS Optimization Guide
Have a look through this list and adjust your BIOS settings accordingly. Possibly the most important thing you should do is disable any unused devices in your system. This will mean that Windows doesn't need to assign resources to these devices and therefore your system wont suffer from sharing IRQ's with devices that you don't even use. This will also reduce the risk of conflicts in your system.
Just remember that no amount of Windows tweaking will save you from a poor BIOS setup. It may take some time, but it's well worth the effort, and chances are that your only ever going to need to do this once.
UPDATING THE BIOS
If you've had your motherboard for a while, then it's likely that new BIOS' have been released that will increase the performance of your entire PC and iron out any minor/major issues with previous BIOS releases as well as increase compatability with newer hardware.
A degree of caution should be taken when updating your BIOS however, as screwing this up can and will render your system unusable unless the correct steps are taken in order to prevent this from happening. This is why you must take great care in making sure you download the correct BIOS for your EXACT motherboard brand, model number and release version. To do this, either open the box and have a look on the motherboard for this information and/or use a system information tool such as Sandra or CPU-Z that should be able to detect this for you.
UPDATING YOUR FIRMWARE
Almost every electrical device in your house has a BIOS chip in it. You're TV, your dvd player. Even some toasters have a BIOS these days ^_^
What this means is that other pieces of hardware in your system have BIOS chips of there own, including but not limited to your optical drives. Make sure you get the latest firmware updates for all of your CD, DVD, DVD-R etc drives so that they are running efficiently. This can also improve compatability with various media that your drive couldn't previously read.
IRQ's (Interrupt Requests)
These enable your CPU to interact with the various components on your system, but sometimes it is necassary for components to share the same IRQ. The idea is to limit this as much as possible as if too many devices are sharing the same IRQ, system instability/performance hits! The easiest way to do this is to make sure you disable any and all unused devices in the BIOS settings. So for example, if you have a sound card, make sure you disable your onboard sound, if you have a network card, make sure you disable onboard networking etc. If you never use any of the legacy connections on the back of your PC such as the seriel port, mini port or game ports, disable those too. If your not using all your IDE/SATA channels disable the ones your not using, this will inveriably make your system quicker to boot, and free up more IRQ's for the devices you do use resulting in a lesser chance of hardware conflicts.
A small note worth mentioning is that all of this is best done before Windows is installed for maximum effectiveness, as once Windows has allocated IRQ's, disabling them in the BIOS later wont remove these allocations.
Hope this helps, and I plan to add more guides for performance improvements in the future.