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Use the CD that comes with the motherboard to ensure everything works driver-wise. In Windows 7, GPU and motherboard drivers come in as optional Windows updates in the Update Center, so you should be up to date on the most common components.
To pick and install the most commonly used apps for your new computer, use Ninite.com. You pick what you want, it spits out an installer that's a couple of kb is in size, and downloads and installs everything in the background using default options. It won't install any bundleware that's normally included with any of the programs.