I think the Bayeux Museum gives a decent overview. Other museums tend to focus in on a particular area, country, or technology, so it may depend on your interests. Here are some I recommend going from West to East:
Azeville Battery—This larger German gun emplacement offers a walking tour inside the bunkers and tunnels. Fascinating look at the life of the German Soldiers working these defenses, and the artillery battles between ships and shore.
Utah Beach Landing Museum—This is my all-time favorite museum in the area and covers this western end of operations, including civilian life in Normandy under occupation, and naval operations off shore. It is inside a German Bunker that was captured on this beach.
Airborne Museum in Sainte-Mère-Église—Covers mostly U.S. Airborne Operations.
Normandy Victory Museum—Covers mostly U.S. operations in between Utah and Omaha beaches, and has a good "virtual reality" exhibit.
Overlord Museum outside of the American Normandy Cemetery—Fantastic collection of all sorts of vehicles used in Normandy.
Musée du Débarquement in Arromanches—I haven't been since they completely remodeled it, but among other things, it covers the artificial harbors that were built and towed into place for off-loading of supplies. The remains of these can be seen right on the beach and off shore outside of the museum.
Arromanches 360° Circular Cinema—great 3D exhibit, and you can walk down the hill to the Arromanches beach and see the artificial harbor remains from this nice, hilltop location.
Juno Beach Center—Concentrates on the Canadian soldiers who landed on this beach.
Musée du Débarquement in Ouistreham. Built into a tall, concrete German artillery observation bunker, gives a good feel for the German defenses in this area.
Memorial Pegasus in Ranville. This covers British Airborne operations, including the heroic capture of the draw bridge over this canal, which was done by crash landing three gliders right at the foot of the bridge. The original drawbridge is on the museum grounds.
Memorial des Civils dans La Guerre in Falaise—This museum is focused on the civilian experience in Normandy.
I am sure I am missing many—some intentionally that I don't think are worth the visit (Caen Memorial and Memorial Museum of Omaha Beach)—and some just because I forgot to mention them. Of course, there are many sights that are not technically museums that are very worthwhile. I do agree with the above comment that you do yourself a favor by learning the big picture history of the Battle for Normandy before going. A couple hours with a good movie or book will pay off in spades, and let you spend more time seeing and understanding the sights, rather than getting a history lesson. Bon Voyage!