1. Use an SSD, it makes a huge difference in speed. I saw over 3x faster load times on large sample based vstis.
2. If you use an SSD, DO NOT run it in anything other then AHCI mode, running it as a raid will cause HUGE stability and performance issues. If you are currently set to a raid setting in the BIOS, reply for steps to change it without having to reinstall windows.
3. Disable network (NIC) card in device manager. This solves many audio issues (static, drop outs).
4. Disable all unused audio components. Especially video card and hdmi audio devices in device manager. On-board audio should be disabled in BIOS.
5. Be sure you have the newest BIOS, usb, pci, and motherboard chipset drivers installed. Check manufacturer website for branded systems.
6. Remove all background apps that are not necessary for audio production. (Do you really need an ISO mounter, various updaters, bonjour, and an Apple itunes/ipod listener running in the background while working in Sonar?)
7. Disable power management in BIOS and windows.
8. Be sure Sonar is set to always run as administrator.
9. Keep your usb ports and fans dust free, and if you are having usb connectivity issues, running short, high quality (thick), and ferrite filters on the cables helps a lot. If your usb bus is running a lot of power draining usb devices, you may need to add a external powered hub to provide more juice for all those usb items that manufacturers think are free to use all the power on those limited ports (stupid modern usb only powered audio equipment is stupid, as most studios use multiple audio equipment).

Too bad constructive posts don't encourage people "piling on" with additional constructive tips...so I'll add a couple, just to be contrary.
 
10. Make sure your power supply is rated adequately. Off-the-shelf computers tend to skimp, so when you upgrade your 4 GB of RAM to 32 GB, add a couple PCI cards, and load up the USB buses...'nuff said.
 
11. An uninterruptible power supply is a must-have accessory. 
 
12. Add a USB port card (not a combo USB/Firewire card) for your USB audio devices. Use the motherboard's USB ports for "dirty" devices like hard disks.

I do not run as administrator anymore. Avoiding old 32bit plug-ins is the easiest way avoid that issue.
 
13. I do set up exceptions in the virus scanner to skip real time scanning for SONAR and VSTScan. Also the project folder. Recently added the control software for my interface too.

Don't forget to be a Caveman & have your club or spear ready when all else fails!

I'm pretty sure there is a very large best practices thread somewhere in the forums. I can't find it but I do remember it. If anyone finds it, a link here may be helpful.