Here is a thread from last year which covers this.http://www.tomshardware.com/forum/22055-63-what-difference-version-retail
Basically, the OEM version is going to be tied to that computer. I think they typically do this by tying it to the motherboard in the system. If you build a new system as an upgrade, you will need a new OEM copy of windows. The retail can be used again in a new machine, so long as the old machine is no longer in use. (Can't have two copies of the same windows at once.) As for functionality for the user, both will be exactly the same, and both can be used on a brand new build.
As for the motherboard dying with the OEM version, you may need to contact MS if the replacement is not the same.