If you have any Silverlight Web Resources in your site map that are hosted by an HTML Web Resource, you may find that when you upgrade to CRM2013 and use the pull down Application Bar the Silverlight page is rendered on top of the navigation buttons so that they are obscured and hidden from the user.
It might look something like the following:-
To fix this you need to adjust the Windowless property in the Silverlight object:
<object data="data:application/x-silverlight-2," type="application/x-silverlight-2" width="100%" height="100%">
<param name="Windowless" value="true" />
Other than this I've not had any issues with Silverlight in CRM2013 but there is now a nice phrase in the SDK that states:
"Microsoft Silverlight web resources remain supported in Microsoft Dynamics CRM 2013 and Microsoft Dynamics CRM Online for backwards compatibility. For components that will be able to be presented on all clients, we recommend using HTML web resources with HTML5 instead of Silverlight."