The KCS Christmas train has one, O scale/O27 I think, in a boxcar.
The New Braunfels Railroad Museum has a N scale and HO scale layout in the old I&GN/MP station.
NBRM
The Meridian Model Railroad Club (Meridian, MS) has a nice HO scale layout in the old REA building of Union Station there.
Meridian Railroad Museum It's pretty nice, and all DC.
The model railroad club in Temple (IIRC, the Cen-Tex model railroad club) has the old Moody (ATSF) depot.
There is a layout in the depot at Foley, AL in the old L&N station there. Also, in Jackson, TN, there is a nice layout in the old NC&StL depot there too.
Finding a model railroad in a depot is more common than a freight car, I think.
Oh, and forgot about the San Angelo club at the old ATSF depot (Kansas City, Mexico and Orient).
San Angelo Railway museum