*If I missed any steps, please let me know in the comments!*

The PC hardware has been assembled, boots, and everything appears to work. The question remains what to do to get it running most quickly and efficiently.

Fresh Install Outline
1 - Install OS (Operating System)
2 - Update Drivers
3 - Update Applications
4 - Install Antivirus Software
5 - Install Spyware Blocker
6 - Install Common Software (Flash, Adobe Reader, etc.)
7 - Install Desired Software (Firefox, World of Warcraft, etc.)

1 - Install OS - Now that the PC can boot, insert what is called your "Live CD," this is the bootable CD that came with Windows XP, Vista, Ubuntu, or whichever OS you have elected to install. This is a fairly self-explanatory, step-by-step process explained by the program during installation. While this is the longest step, it is generally the most trouble-free.
Ubuntu Note - You may need some assistance installing Ubuntu when you get to the section on partitioning. This is available in the Ubuntu forums.

2 - Update Drivers - Self explanatory? Not necessarily, you should visit the Realtek website to update your motherboard audio codec, the Nvidia or ATI site to update your respective graphics card drivers, the manufacturer's website for your DVD and CD burners and readers to update their firmware, and even your expansion cards. Firmware updates to your burners, in particular, can improve noise levels, write ability, and read ability.

3 - Update Applications - Download the latest versions of Internet Explorer, Windows Media Player, and the other software that is part of your PC's core. This may be a package like Windows XP Service Pack 2, or piecemeal by necessity in Ubuntu. Either way, you should have the latest version of your software installed to ensure maximum compatibility with existing file types and internet applications.

4 - Install Antivirus Software - If you do not want to pay for McAfee or Symantec software, there is reputable free antivirus software out there such as AVG or Avast! (pirate not included).

5 - Install Spyware Blocker - I use only Spybot Search & Destroy, it is the most reputable (and free) online spyware monitoring and removal tool (at least that I am aware of).

6 - Install Common Software - Installing the following software early-on will make your life easier than installing it on the fly: Adobe Flash player and Acrobat reader, Quicktime (though you do not necessarily need iTunes), a video codec package from a site like Free Codecs, and anything else you might use regularly.

7 - Install Desired Software - Go nuts; your computer should be fighting fit, at this point. Congratulations!