There are over 200 museums in London. Here's my pick. If you want to see a list of all look here.
I've written down each museum's website, the nearest Underground station and a reference on a Google map to make it easy to find. There is also a price for paid museums, but it is approximate so that you know how to consider it. The price may have gone up in the meantime, but discounts may also apply to children, families, students and seniors (most of the time, feel free to ask).
National museums are free in London (donations may be collected and special exhibitions may be chargeable).
The museum is huge. If you watch every exp for 15 seconds, it would take you a few years without days off to watch everything. Special emphasis is placed on the historical findings of ancient Egypt, Greece and Rome. There is no hope of seeing everything, but the overall impression is powerful.
Everything possible related to nature. From dinosaur skeletons to butterflies.
Over 2,000 paintings from the Middle Ages to the present day. Da Vinci, Botticelli, Caravaggio and Van Gogh.
Everything related to science. Reconstruction of the first (mechanical) computer, Apollo lunar landing capsule, Watt's steam engine. Lots of interesting things for children too. My favourite.
Over 2.5 million artworks and design objects. One of the largest collections in the world. Fashion, furniture, sculptures, jewellery and more.
Modern art. It is located in a converted building of an old power station. Suitable for a visit together with a visit to St Paul's Cathedral, as they are connected by a pedestrian bridge - the Millennium Bridge.
Everything about London from ancient times to the present day. Interesting stuff, but with an ugly messy structure. You want to go see something according to the sign, but it leads to a dead end corridor or back to where you came from.
Facts about wars from WWI to the present day.
Maritime history. Old maps and ship models. Admiral Nelson's uniform as he wore it at the Battle of Trafalgar.
Toys, dolls, board games - everything related to childhood from 1600 to the present. There are also indoor attractions that children can participate in.
Home of a famous architect. Lots of paintings and antiques.
Contains an old amphitheatre found during excavations when the gallery was built.
18th century French art. Titian, Canaletto and Rembrandt. The building itself is also worth seeing.
The largest collection of portraits in the world.
British Art since 1500.
Changing British homes through the ages. Each room is decorated in the style of a different era.
Science, medicine, psychology. Darwin's walking stick can also be seen. :-)
The history of London as a port city.
The old prison. Quite a terrifying place where you can get a picture of yourself behind bars as a souvenir.
Vehicles, photos, posters, sound recordings, maps, uniforms, badges, films and videos. Everything related to transport in London.
Any design from cars to three-legged stools.
All about the British Air Force.
Underground spaces from where the country was run during the war.
World famous wax museum. Several statues are made from "originals" because Madame got her hands on the severed heads of many celebrities.
Battleship, anchored forever.
Over 10,000 items related to the famous writer.
The infamous Henry VIII was born in this house.
History of banking and money.
History of the Jewish People. Judaism. The Holocaust. And many more...
You cannot see the whole palace, only a part is open to visitors.
"Museum" of a famous book character.
Unfortunately, it is only open on the first Sunday of every month. :-(
An incredible number of musical instruments. Also documents, pictures... Many famous Cremona string instruments and if you're lucky, you can even hear some of them.
Postal matters. A lot is especially designed to make it interesting for children.
A 19th century operating theatre located above the church. Various surgical techniques are demonstrated.
Over 12,000 parcels, boxes, cups... from the era of Queen Victoria to the sixties of the 20th century.
Harry Houdini and others...
Steam engines and locomotives. If you want to see these in action, plan your visit for a day off or a Bank Holiday.
More for medical enthusiasts. All about pain and painkillers.
Marc Isambard Brunel and his son Isambard Kingdom Brunel were the engineers who first began to build large tunnels under the river.
London's canals, shipping and freight on these.
Animated films and comics.
Everything from the cinema. Just from the cinema, not from the films. Posters, decor, seats and even bits of carpets.
18th century house. Its ten rooms have an air of the past, as if the residents had just left here.
Fans from the 11th century. Located in two nice 18th century houses.
Sigmund Freud settled in this house in 1938, having fled from the Nazis in Vienna. The entire interior has been preserved, including the famous sofa.
Museum of Engineers and Technology Enthusiasts. Among other things, a 116 ton fully operational 'test machine'.