Joshi Railway Museum, near Karishma Housing Society, Kothrud. Website: http://www.minirailways.com/

Kelkar Museum, on Bajirao road (halfway beteen Swar Gate and Shaniwarwada). Random collection of stuff that Raja Dinkar Kelkar liked. Raja Kelkar Musuem is probably the best museum on Maratha/Peshwa History. Its truely fascinating. Do checkout this link: http://www.rajakelkarmuseum.com/index.asp

Another great place for Pune history is the museum and exhibits at Bharat Itihaas Sanshodhak Mandalin Sadashiv Peth, off Tilak Road. They have a great collection of paintings, books, coins (some dating back to over 2000 years). http://en.wikipedia.org/wiki/Bharat_Itihas_Sanshodhak_Mandal

The museum on Parvati is a must-see for children. Heritage construction, household equipments, ornaments, clothes, instruments, armament, and photos of old Pune are a treat for children. They can learn so many things while enjoying the trip to Parvati.

Fort Jadhavgadh Heritage Hotel also has a good small museum about Maratha History. http://aparanjape.wordpress.com/2008/11/04/hotel-review-fort-jadhavgadh-heritage-hotel/

Phule Museum on Ghole Road (haven't visited this place in years).

There is a small museum in sarasbaug Ganpati temple that houses different styles of Ganpati statues and images.

Raja Kelkar Museum! :)