This is the MSDN article "Upgrade Code in the ISV folder to Microsoft Dynamics CRM 2011"
But the one thing it doesn't mention, gave me hell today.
In multi organization deployment you need to include the organization name in the path to the isv folder.
in mscrm 4.0 the path was:
In 2011 the path needed is
otherwise it tries to authenticate the user with the user's default organization which might be different then the one needed.
http://nishantrana.wordpress.com/2011/03/17/showing-a-custom-aspx-deployed-in-isv-in-iframe-of-crm-form-crm-2011/. Without it I would have kept struggling with the code upgrade for quite some time.
One last thing:
It is better to really upgrade the code in ISV folder into something that stands by its own like WebResource(HTML, Silverlight) or separate asp.net application with it's own application pool. The ISV folder is officially deprecated.