Startup File

Now that you have set up your User Preferences and have gone through the Properties Setup, I have a couple of suggestions that may make your Blender experience a little bit better.

1. Clean up the desktop a bit by moving the Camera and default Lamp to another layer. I generally move them to the last layer, a.k.a. the junk layer, to get them out of the way. To move an object, select one by right-clicking (RMB), or multiples by holding Shift + RMB. With your arrow cursor still in the 3D window, select the M key to move, and choose the layer you want to send them to.
2. If you haven't done so already, switch the render engine from Blender Render to Cycles Render. After doing this, Blender changes the way it creates the World and Materials. Be sure to select the World Settings and Material Settings in the Properties Window and select the large button that reads Use Nodes in each.
3. Make any other changes you'd like to be part of your Startup File.

You are now ready to save your Startup File that will keep all your settings that you configured as the default settings.

All you need to do is select File > Save Startup File. You can also use the keyboard command, Ctrl + U. You will be prompted to confirm your selection.

If you ever change a setting that you want to be part of your Startup File, simple repeat the above step.