I am thinking of adding a chair rail in my dining room, but I don't know how high it should be. Is there a standard height? Also, how do you deal with doors and larger openings without doors (like between the kitchen and dining room)? How about windows? We have standard size double hungs that are 32" from the floor, with the bottom of the window frame at 29" from the floor. I should say that I want to use a different color on either side of the rail.
Thanks for your help!

Chair rail height is anywhere from 32-36" off the floor. When the chair rail comes to a door, just butt it to the door casing. When it comes to an archway you can cut a return for it or cut a 22 1/2 inside miter just to give it some end detail. At the window, butt the chair rail to the window casing.
As far as painting, you can paint the chair rail, then your 2 different colors before installing the chair rail then you don't have to worry about cutting in or you can install the rail then paint the walls & rail.
Before you install the rail find the stud locations and mark them on the wall so you know where the nails go.

I always install chair rail 32" center of chair rail, this allows for different width molding.

Doors or openings you can back cut at 22degrees or stop 2" from the opening and cut the molding as if you were turning a corner, this looks good for the thicker molding, in case the chair rail is thicker (fatter) than the door casing. This will put the design of the chair rail on the return, it will be a small piece use a brad nailer or elmers carpenders wood (school) glue, masking tape to hold it till the glue dries.