Where to by the Paris Museum Pass?

Don't buy it in advance; they overcharge you! The best places to buy are the less-frequented attractions like the archeological crypt on the Parvis de Notre Dame, or the Museum du Moyen Ages at the corner of Blvd. Saint Germain, and Blvd. St. Michel.
Any particular place can be sold out on any given day since there is such a high demand for the passes.

You can buy it at most of the locations that it's good in...not the Archaeological Crypt though--when we tried that, they directed us to a nearby shop, which was fine. You should avoid buying it at the bigger places though because you will have to wait in line, which kind of defeats one of the main reasons to buy it. No need to buy it in advance.

The Orsay Museum has a separate desk for buying the pass, and you don't have to wait in the main ticket line. If you face the main entrance from outside, you'll see it off to the left.

If you are arriving at CDG, then you may happen to pass a TI while on your way out. We found one, no line at all, and completed our purchase in just a few minutes. This was following the direction signs from our arrival terminal to the RER. As I lost my pass, carelessly in the same pocket with my daily cash, I purchased another at the Cluny just before closing. No line there either.

I'd go with Bill's suggestion about the Musee du Moyen Ages which is one of my all-time favorite museums in Paris. Very intimate look at some of the stonework and stained glass from St. Chappelle and Notre Dame because they put pieces that had to be removed due to damage and put them in this museum at eye level.

I always buy my passes at the ticket area in the Louvre. I enter through the carousel (mall) entrance (not the main entrance at the pyramid). I don't recall having to wait in a long line to buy the pass.

BG, they moved the location at the Louvre.
If you go down the pyramid (after security) head toward the Starbucks cafe (yes, Starbucks in the Louvre!). Across from Starbucks is a glass office. You buy the passes there. They accept plastic and cash.