In CRM 2015 update1, We can change the theme of our app.
To do that .
Settings –> Custmoizations –> Theming
You will find one theme which is default.
Open that and Click on Clone from Ribbon, It will clone the default one and opens it for you.
You can change colors and also can choose your Logo
Once after you update your theme, You can click on Preview to see with out surprising your current users.
Once you see everything is good , click on Publish Theme.