I second the recommendations for The Museum of Jurassic Technology in Los Angeles and The Glass Museum in Takoma, Washington.

The American Visionary Art Museum in Baltimore, which specializes in outsider art, is interesting and is especially good for their special events (e.g. the kinetic scupture race).

I spent the better part of a day at the newish Musical Instrument Museum in Phoenix.

In general, I can enjoy almost any small town history museum. They usually have an odd mix of historical photos and collections donated by local people. The one in Loudon County, Virginia (Leesburg to be precise) has an interesing collection of letters written by former slaves who emigrated to Liberia to their previous masters, for example.