As the list of ghoulish museums gets longer, I can't leave out the
"catacombs" of El Covento de San Francisco in Lima, Peru.  This is
a historic church (still functioning as a church and convent), but
they have a small museum upstairs (street level) with some beautiful
artifacts from the time of the conquest, and in the basement what
they call the catacombs--an enormous collection of skeletal remains,
many artfully arranged in pleasing geometric patterns.  When I was
there years ago, tours were only available in Spanish, but it was
a very good tour, and tastefully handled.  I have since seen images
of the bones in the catacombs on several television shows dealing
with Latin America, religion, etc.  Just a short walk away from
San Francisco, you can visit the Catedral de Lima and see what is
reputed to be the corpse of Pizzaro (not likely, apparently), and
a few blocks from there, the museum of the Court of the Inquisition,
which does contain a nice set of equipment for torturing people.
 
John Simmons
Musuem of Natural History, University of Kansas