On the Tools – Options – Environment – Import / Export Settings (yes, the Tools – Import / Export Dialog has its own Tools Options page), you’ll find the option where to store you current settings. Note that you don’t get to opt out of this. Prior to 2005, setting categories were saved in separate files in %appdata%, like a file for all your toolbox customizations, your window layouts, your keyboard shortcut bindings, your command bar changes, and so forth. Starting in 2005, those settings are now stored in a centralized file, the .vssettings file.
Every time VS shuts down, we write out to this file location to keep your current settings current.
If you ever make a change that you need to quickly back out of, you can always go to Tools – Import / Export Settings – Import and choose the CurrentSettings.vssettings file located under the My Settings node/folder. This maps directly to the file under Tools – Options – Environment – Import / Export Settings