We're in the middle of a massive SP2007 to SharePoint Online migration and were able to successfully rebrand our portal site in the cloud. The only portion we're having trouble with is matching our "mysites"'s branding with the portal branding. We can't seem to find a way to do it at all. Is it possible to do and can someone point us in the right direction?
You are able to brand the My Site host itself (where Newsfeed is) with SharePoint Designer. However, each SkyDrive site (My Content site) is a separate site collection. You would need to manually apply your branding to each one individually. Not ideal, but Office 365 and SharePoint Online don't give you any other options. If you have SPO-D (SharePoint Online Dedicated) you can create a custom branding solution with feature stapling, etc., to activate a feature that applies the branding for each SkyDrive site. They have a rigorous approval process for getting custom solutions into their SPO-D environments, but it is doable.
You can apply branding to existing mysites using a provider hosted app and CSOM. Check out Vesa Juvonen's video (http://www.youtube.com/watch?v=rht3pSe34O0) and blog (http://blogs.msdn.com/b/vesku/archive/2013/08/23/site-provisioning-techniques-and-remote-provisioning-in-sharepoint-2013.aspx) on the subject