Searched the communities and documentation, and can't find a place actually tells you where and how to change this. Found this out with hard way. I thought this would be helpful lots of people.
1. The style sheet for the logo is actually stored in web.war. So, you might want to unzip it under gatein.ear, and then move the web.war else where.
2. Change the web.war/skin/portal/webui/component/UIBannerPortlet/DefaultStylesheet.css, or create your own stylesheet. Change the logo gif in .UIBannerPortlet .RightBanner class. Make sure you need to have /* orientation=lt */. I think GateIn dynamtically generate the style sheet. You can see this from the view source of the home page. Without this flag, the attribute will not be generated.
3. Adject the .UIBannerPortlet .MiddleBanner height for your logo size. Again, make sure you put /* orientation=xxx */
4. You need to restart the server to see the change as the stylesheet is generated dynamically. You can see the actually stylesheet generated by the View Source.