Definitely the Wasa Museum. It`s a warship that sank on it`s first voyage in Stockholm Harbour and was raised to the surface in 1961. Really brilliant.
A trip out around the islands is also excellent.
I didn`t have long enough there, so others will come up with loads of different things for you.
I went there on a girly weekend we took the open top bus tour and the boat trip which was very good. Also take a visit to the ice bar, a bar literally made of ice.