The museum is on the main street in Valletta, Triq Ir-Repubblika, it's identified by flags outside, and is only a few minutes walk from the crazy bus terminus. Open daily 09:00 - 19:00 (last admission 18:30) and costs 2.33 euros (seniors and students 1.16, children 0.58, 5 and under free). There are currently guided tours in English every day at 10:00 and 15:00 at no extra charge. There's a well stocked shop and visitor toilets. Officially there's no photography inside, but no one seemed to mind me taking pictures without flash.
I had arrived a little later than planned due to a long wait for a glorious 1960s Bedford bus and some crazy traffic, but tacked onto the 10am tour less than half way round and was very glad I did - a very well informed guide explained the temples and their finds with a fair amount of humour too.
The first part of the museum (nb only the ground floor is open - but seeing as it's this floor which covers the prehistory I wasn't bothered that the planned expansion upstairs and galleries on Phoenician and Roman culture, through 1800 CE, were still unfinished) explains the cronology of the period covered (5200 to 2500 BCE) and the possible construction techniques used, before moving on to look at most of the main sites in order and in detail, with fabulous scales models to see.
Some information about the finds:
there are loads of headless bodies, with sockets where the neck should be, to insert a choice of heads (from Hagar Qim); a green stone cylinder with gold inlay (unique to the islands) and red stones inset (from Tarxien); a sherd with a solar wheel decoration (from Hagar Qim); the Venus of Malta; a clay statuettte of a pregnant woman and a whole display case of stone carved and clay phalluses (maybe the temple builders were indeed part of a fertility cult); and most importantly, the "Sleeping Lady" found at the Hal Saflieni Hypogeum.
The largest room is devoted to the Tarxien temples, and has many of the original spiral carved stones, moved to the museum to prevent damage from weathering - replicas are now in situ there. Many of the stones are shown alongside photos of their excavation.
The museum building is the Auberge of Provence, and the guide explained its history with the Knights of St John in the 16th century.