The logo image is referenced in many places: css files, htmlheader.vm and rss feeds (possibly others). The name of this image is hardcoded to logo.gif, which is not the case anymore, since the new skin uses a png file.
We should add a new field either on XWikiSkin for specifying the right filename, and use this property when needed.
$xwiki.getSkinPreferene("logo")or, if a default value should be used if the current skin does not specify a logo: