The Add On to let you brand FreeCMS as your own is almost complete. I'd expect we'll launch it in the next 2 - 3 weeks, and it will be awesome!
We've introduced a new concept into our site called a 'Theme'. You can create as many themes as you need. A theme allows you to customize the color scheme used by FreeCMS as well as the logo. It also lets you specify a url used to access FreeCMS when viewing a theme. You can have a subdomain of cms-admin.com (e.g. yoursite.cms-admin.com) or if you control the DNS of your site you can set up your own url (e.g. cms.yoursite.com). We'll allow more customization in the future, so let us know where you'd like more flexibility.
Once you've created your theme(s) you can start using them. You can edit your Profile and add a theme so that whenever you access FreeCMS you see the color scheme you'd like to see. You can also add a theme to a Website so that when an Editor goes to edit their site they see their logo and color scheme. Not only that, but you can use the code we give you to create an iframe in the website so that FreeCMS looks 100% integrated into their site. The best part is that each Website can have its own theme so you can give each client a totally customized experience!
There are even more exciting features, but we'll save that for release time. If you have any feedback please let us know and we'll do our best to incorporate it.