Paris has a plethora of museums.  The Louvre, the Musée d'Orsay, the Rodin Museum, the Pompidou, the Picasso Museum, of course.  But what others?  I recently stumbled across Wikipedia's entry for all the museums in the city.  I've visited some of the lesser-knowns, but have yet to see all the ones that interest me.  Here are some that I've visited and some of the more unusual ones that I've yet to see.

• Musée des Lettres et Manuscrits - Located in a townhouse from the 1600s, the museum displays original works by Descartes, Voltaire, Diderot, Stendahl, Flaubert, Zola, Verlaine, Nadar, Magritte, and plenty of other Frenchies.  They also have some manuscripts/letters from Mozart, Beethoven, Chopin, etc.  See the Wikipedia entry for a full list.
• Palais de Toyko - Not sure exactly what's in this museum, but I've walked past it many a time.  It's very close to the Eiffel Tower, and I think the building in which it is housed serves as a kind of Japanese cultural center for the city.  Looks very interesting.
• The Catacombs - Paris's ossuary, which was primarily used during the years of the Plague, I believe.  Essentially, underneath the city in a series of tunnels there are thousands of bones piled neatly on top of each other.  If you visit the city during the summer, this is a great place to escape the heat.

• Musée de la Poste - A postal museum that specializes in the postal history and philately of France.  This one's high on my list, but I've yet to visit.
• The Jeu de Paume - A museum of modern art not far from the Louvre.  I don't know much about their permanent collection, but since September they've had two incredible photography exhibits: one of Avedon's work and one of Lee Miller's.  I think they frequently host exhibitions of high-caliber photography.
• The Gobelins manufactory - Not far from where I live, this is a small manufactory where tapestries are made.  The Gobelins were a family of dyers who began business in the city in the 15th century.  I believe tours are only offered in French, but a tour is the only way to see the actual manufacturing process -- otherwise, you can only see the show rooms.
• Musée d'histore de la médicine - I've yet to visit this one, but I hope it's akin to Philadelphia's Mutter museum.  It houses one of the oldest medical collections in Europe.
• Musée de l'erotisme - Paris's erotic museum is located in the heart of the red light district, near the Moulin Rouge.  On display are sculptures, figurines, toys, a few costumes and furniture, as well as a collection of drawings.  Most interesting, perhaps, are photos of (if I remember correctly) the interior of an old Parisian brothel -- photos made on glass plates.  Though they don't exactly compare to Bellocq's work, they bring it to mind.  Though the museum has seven floors, one can easily see everything in about an hour, two for slowpokes.