Changing the logos & brand name from Etherpad to your own requires modifying the following files:
(Images)
/usr/local/etherpad/trunk/etherpad/src/static/img/jun09/pad/protop.gif
/usr/local/etherpad/trunk/etherpad/src/static/img/jun09/pad/padtop5.gif
/usr/local/etherpad/trunk/etherpad/src/static/img/pro/header/pro-header-logo.png
/usr/local/etherpad/trunk/etherpad/src/static/favicon.ico
(Text)
/usr/local/etherpad/trunk/etherpad/src/templates/main/home.ejs
/usr/local/etherpad/trunk/etherpad/src/templates/html.ejs
/usr/local/etherpad/trunk/etherpad/src/templates/pad/create_body.ejs