As you mentioned, GRE supports encryption but it is not a secure tunneling/encapsulation protocol.
At the same time there are limitations to IPSec: it can not carry non IP protocols such as IPX and AppleTalk. IPSec tunnels also can not normally forward routing protocol traffic such as OSPF and EIGRP. That is why -I think- most IPSec configurations are referred to as LAN-to-LAN (using static routes for each SA).
In a nutshell, use GRE with IPSec if you are routing IPX/AppleTalk or if you have two routers that need to exchange routing PDU's through the tunnel.
Configuration Example:
http://www.cisco.com/en/US/tech/tk583/tk372/technologies_configuration_example09186a0080093f85.shtml
Regards,
Mustafa