Poland is not really renown for its museums. The city of New York probably has more artwork than the whole country; indeed, the Louvre probably has more (and only displays something like 10% of it's collection at a given time.) Much of it was either burned or looted during WWII and not everything was recovered.
Krakow boasts a beautiful Leonardo Da Vinci (Lady with Ermine), and used to have a Rembrandt (it went missing in the forties.) The Sukiennice also held a nice collection of paintings before it was closed for renovations (it won't be open until 2010.) The Wawel has a very nice collection of Ottoman war treasures that were seized when King Sobieski came to the aid of Vienna in 1683.
The National Museum in Warszawa is worth a visit and is quite sizable. They have a variety of artwork and historical artifacts, ranging from the ancient Egyptians and Greeks to the early Christians of North Africa. They also have a good collection of Polish art. This includes the jewel of the museum (in my opinion) Battle of Grunwald by Jan Matejko.
Kasia in front of Bitwa pod Grunwaldem
One place not to go for museums, is Kazimierz Dolny. The Museums here are worthless, overpriced (the giant museums of Warszawa and Krakow are cheaper) and have collections that are dwarfed by most high schools.