SharePoint branding is one of the most controversial subjects on SharePoint world. There are pros and cons of doing it and there are several different ways to apply your brand to SharePoint as explained in this article.
Branding is often used to change the way SharePoint looks like and to make it aligned with the corporate visual identity. Doing this type of customizations can bring extra functionalities to the product and most importantly can increase the user adoption of SharePoint.
Besides all the positive aspects it can also have a negative impact on SharePoint if not done correctly depending on the branding method used you can easily loose default functionalities or even worse break the entire site.