Some ideas of the places to visit on your own and/or with the children:
1) Moscow Darwin Museum
www.darwinmuseum.ru Akademicheskaya metro station
2) Экспериментариум
http://www.experimentanium.ru (There is an English version of the website) Sokol metro station
3) Live systems museum
http://www.bioexperimentanium.ru/ Savelovskaya metro station
4) Moscow railway museum
http://www.rzd-expo.ru/museums/museum_of_the_moscow_railway/ (There are two sites: one at Paveletskaya, another at Rizhskaya metro station)
5) Space museum (Museum of cosmonautics)
http://www.kosmo-museum.ru/?locale=en (There is an English version of the website) VDNKh metro station
6) Музей техники Вадима Задорожного
http://www.tmuseum.ru/ : Vadim Zadorozhny’s Vehicle Museum is one of the largest in Europe and the largest in Russia private museum of vintage technical equipment. The best antique machinery of the last century was being collected here diligently during the long time: military hardware, weapons, aviation, motorcycles, and of course retro cars - more than 1000 exhibits. Vadim Zadorozhny’s Vehicle Museum can rightfully be called now a national-level cultural project. Tushinskoe or Strogino metro station
7) Музей индустриальной культуры (Museum of industrial culture ) Not an ordinary museum
http://www.museum-ic.ru/ Liublino or Volzhskaya metro station
8) Orlov Paleontological Museum
http://www.paleo.ru/museum-en/ Konkovo or Teplyj stan metro station
9) Theater "Уголок дедушки Дурова" (for the kids starting from 1.5 y.o
https://www.youtube.com/watch?v=53EDCuPRNl8 Spectacles with the animals) Official website:
http://www.ugolokdurova.ru/ Tsvetnoj bulvar metro station
10) Nikulin curcus
http://circusnikulin.ru/ Tsvetnoy bulvar metro station
11) Tretyakov gallery
http://www.tretyakovgallery.ru/en/ (English version of website)
Just to keep for memories