This post is intended to be a dumping ground that I'll update as and when I, or my colleagues, find issues that may affect the upgrade of CRM 3.0 implementations with client script.
RemoteCommand - removal of some options
In CRM 3.0 it was possible to make unsupported use of the client-side RemoteCommand function to make server-side calls, e.g. the following got the current CRM user id
var cmd = new RemoteCommand("SystemUser", "WhoAmI", "/MSCRMServices/");
var res = command.Execute();
What this did was make a request to the SystemUser.asmx (1st parameter) file in the MSCRMServices (3rd parameter) directory. Almost all of these files have been removed in CRM 4.0, so code like that above will fail.
I can't see any obvious equivalent calls to make in CRM 4.0, but as the use of RemoteCommand is unsupported, I wouldn't expect there to be. My preferred option has always been to write a server-side wrapper around calls the CrmService web service, and call them directly using the XmlHttp ActiveX object, thus keeping within supported functionality.