First of all I would recommend to use one of the known protocols to tunnel encrypted packets. There are several options and all of them will be successfully processed by routers:
1) IPSEC ESP protocol
As an example you can look at the GRETunnel sample from WinpkFilter samples set. It does not actually encrypt the tunneled packet but it is fairly simple to add encryption. If you need to have an extra information attached to the packet you can also use extended GRE.