Hello Thomas,
if you're talking about the website logo found usually at top left corner, then this is in fact using the websiteIDcard token {$plugin:widcard:bizLogo}. You can either upload your logo there by going to the websiteIDcard menu or remove that token from the html templates (index and others), so that it does not show up at all.
It's pretty convenient to use these tokens, as you can then have all your company information located in one place. When you update it, all your templates update that way.
WebsiteIDcards token also help to build mobile versions of your website, or building automatically your geolocated KML file found at /website.kml. More info about this here;
http://www.seotoaster.com/local-search-engine-optimization.html
You can find a list of system tokens at
http://www.seotoaster.com/cheat-sheet.html