You know wrong. There's nothing that bars water lines passing over panels. The only requirement is that the area be characterized as permanently dry. A pipe doesn't make a wet location. Of course, you have to make sure you're not encroaching on the working space requirements.

 

OK may be my interpretation of this is out of whack.

National Electrical Code 2008
Article 110 Requirements for Electrical Installations
II. 600 Volts, Nominal, or Less
110.26 Spaces About Electrical Equipment.
(F) Dedicated Equipment Space.
(1) Indoor.
(a) Dedicated Electrical Space. The space equal to the width and depth of the equipment and extending from the floor to a height of 1.8 m (6 ft) above the equipment or to the structural ceiling, whichever is lower, shall be dedicated to the electrical installation. No piping, ducts, leak protection apparatus, or other equipment foreign to the electrical installation shall be located in this zone.
(b) Foreign Systems. The area above the dedicated space required by 110.26(F)(1)(a) shall be permitted to contain foreign systems, provided protection is installed to avoid damage to the electrical equipment from condensation, leaks, or breaks in such foreign systems.

By reading it again, does it mean I cannot pass a pipe under 6' but can pass a pipe at 7' from the floor?

and if this "Electrical Equipment" I assume it means a panel, does it apply to a trough box?

 

I mentioned the clear space considerations, but that's not unique to water pipes.

Your trough is a raceway and isn't "equipment" in that sense.

 

What would be considered "equipment" in this context?

I assume a panel counts? A trough does not? How about a switch box or a junction box?

One typical scenerio would be the water line comes into the garage on say the left side of the panel, and the water heater is say three feet to the right side of the panel, so you need to run a cold feed to the WH and a hot one back. You are saying it can run across above the panel (as long as it clears the 6')? I have always only seen it run below, as plumbers have been telling me all along electric code prohibits running above.

In my case if I don't need to worry about the trough then I won't. I do know there are going to be times when it will get wet when I connect/disconnect the manifold ports.