On my sons house, the ground wire runs down from the surface mounted main panel, to the ground rod in a piece of 1/2 inch EMT and exits it with the end of the EMT open. This looks a little strange, is it up to code?

Good question.

A ground wire does need to be connected to the metal conduit, usually with a two screw connector is allowed. There is an EMT to cable adapter available. Or use an EMT connector, rigid couplng, and a cable connector all threaded together.

I've seen it before, but in commercial installations. The conduit is merely used to protect the wire. It has no physical connection to the wire, except where it may contact it. It's not a bad idea, and the ground isn't interrupted by anything since the conduit isn't part of the circuit, just a protection.

Thanks for the help guys...

There is no difference in commercial or residential, a metal conduit with a grounding electrode conductor must be bonded to that conductor.