Modding FAQs Part One - Why don't my mods appear in the launcher?

This series will be a collection of answers to commonly asked questions related to modding, focused mainly on using mods, but occasionally involving creating them as well.

The first question I commonly see asked, as the title states, is some variant of "Why don't my mods appear in the launcher?"

The answer is provided in the first official G.E.C.K. tutorial on the G.E.C.K. Wiki but, many people don't really have any reason to read that, or don't read it carefully enough.

"Don't see your .esp file? Verify that you installed the GECK to the same directory as your retail installation of Fallout 3. The file should have been created in a \Data sub-directory in that directory. This is where the launcher looks for data files.
Under Vista, if you are not running as Administrator, the data file may have been created in a shadow directory (with a name like "\Users\Me\AppData\Local\VirtualStore\Program Files\Bethesda Softworks\Fallout3\Data"), where it is visible to the GECK but not to the Fallout3 launcher. You can avoid this by always running the GECK as Administrator."