Manual:$wgDefaultSkin/ja

Details
This setting defines the default skin and should be set to the lowercase name of the skin (e.g. 'monobook', not 'MonoBook').

Note that this only sets the default skin, for new users and anonymous visitors. Registered users may change this to any one of the other available skins through their preferences page (see Manual:$wgSkipSkins on how to control that).

Changing user preferences when removing a skin
In versions up to at most 1.11, upon registration the value of  was copied to the user preferences; thus setting $wgDefaultSkin to another skin would not have had any effect on registered users, even if they never changed their preferences. And it did not have an effect on registered users, who did change the skin to use.

When you remove a skin from the list of skins to choose from, use the maintenance script Manual:UserOptions.php to make sure that this skin is also not chosen by any user:

This will change the skin for all registered users, who have selected Monobook, to Vector.

Available skins
Several skins are included with the MediaWiki installer tarball (the table below details the versions they were/are available with). You can find more skins in Category:All skins.

The first column gives the ID which should be used to configure this setting, the second gives the name as it appears within the MediaWiki interface and the third indicates the versions of MediaWiki that this skin is available for: