It's not just in Stockholm in all Scandinavian countries there are a plenty of museums. If you are a museum buff then this is Stockholm is the Mecca for museums on earth - head on with the museum pass. I had been to the Vasa Museum, Skansen Open-Air Museum, Music museum, Army museum and the list goes on for 70+. I have mentioned a few, click here to know more about other places.
Let me start with the Vasa museum
This museum exhibits a beautifully preserved ship built in solid oak and pine with wood in 1628 and which sank on the maiden trip. It was salvaged in 1961 in a fabulous. "The Age of Vasa" is a journey in time to the country behind this ship, miniature of the Vasa ship 
The history of Vasa can be read here
Skansen Open-Air Museum is one of Stockholm's most popular tourist attractions with some 150 houses and farmsteads from all over Sweden. Zoo, "Mini-Skansen", summer concerts are a few interesting things.
Music museum - Instruments from a 17th century tavern to the heyday of ABBA all under one roof. You can play many of the instruments here...
Aquaria Water Museum
Worth a visit even on virtual one that's provided in the official site. 
mangroves, Living rainforest all beautifully created
A Boat Sightseeing is worth mentioning
