Speaking of Waterloo, two museums there merit special attention.

Caillou. This building (see photo 7 at right) served as Napoleon's headquarters, and is today a museum to the Emperor's presence at Waterloo. Here you can see the room where Napoleon had breakfast the morning of his last battle [during which he told his generals that the English were bad troops and Wellington not much of a commander]. If you look closely, you will see the bones of the last soldier dug up at Waterloo, now resting where the breakfast table used to be. (The bones of Philip II, Alexander the Great's father, are displayed in a similar fashion in Greece, but at least they are not at the breakfast table!) Also in this museum is the room where Napoleon spent the night before the battle, and the ever popular collection of battle flags.

Wellington Museum. There was this other fellow at Waterloo as well, and his museum is also of interest (see photo 8 at left). This museum is actually quite interesting, with many artifacts of Wellington's visit, including his desk. If you are in the area, both of these Waterloo museums are well worth the effort. [See Mr. Gilbert's review of the Wellington museum in London.]

Musee national du chateau de Compiegne. Home to royalty long before Napoleon, Compiegne provided shelter for Napoleon and Josephine, Napoleon and his second wife, Marie-Louise, and their son the King of Rome. Later, the King [Jerome] and Queen of Westphalia lived there. An enormous building, the chateau houses a huge collection of first and second empire furniture and artifacts. The Emperor's dining room (see photo 14 at right) features a table from 1807, and Napoleon's bedchamber is exactly what one would expect. The Galerie de Bal is dominated by a large marble statue of Napoleon as Caesar (see photo 10 at left). This museum deserves consideration of the highest order.

Museums:

Napoleonic Museums in and around Paris
Napoleonic Museums at Waterloo
Napoleonic Museums in Rome, Monaco, S. France
The Wellington Museum in London
Ultimate Reference for Finding Napoleonic Sites

Related:

The Museo de Risorgimento in Milan, Italy