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Adding the logo was easy.  The "stock" new install of MediaWiki even gives you a clue - the logo says "Set $wgLogo to the URL path to your own logo image".  Yup.  That's what you have to do.

There's a lot of built-in help pages like [http://meta.wikimedia.org/wiki/MediaWiki_FAQ#How_do_I_change_the_logo.3F this one] or [http://meta.wikimedia.org/wiki/Customize_page_layout#Change_logo this one] that tells you what to do.  Search for the variable name $wgLogo.

So get a logo.  Tweak it with GIMP or whatever.  The one I borrowed had a white background.  I used Gimp to make the background transparent.  They tell you to make it 135X135 pixels, so find a square-ish one and make it that size.

Basically you can stick it in any place that your web server can serve pages from.  My web server document root is set to /home/porterg/public_html.  I added an images directory under the document root.  I put the modified logo file there.

I then added this to the end of my /home/porterg/public_html/w/LocalSettings.php file.  This is the "master control file" for the wiki.

$wgLogo="/images/tux-server_clear_bkgnd_sm.png";

Note that the path is relative to the web server document root.