For v4.x, look in ZmSetting.
js located under <src>/ZimbraWebClient/WebRoot/
js/zimbraMail/share/model/
There is a constant called "LOGO_URI" defining the url to use for the logo.
Once you modify this file, you'll have to redeploy the webclient:
- For example, under /ZimbraWebClient, run "ant prod-deploy" to deploy the production build.
This has been simplified for version 5.x - basically, you'll just need to modify the skin.properties file for the skin you want to change. There should be a more comprehensive list of changes once v5 is released.
HTH.