Another of the projects also vying for the prestigious Museum of the Year award - the UK's largest single arts prize - is Feilden Clegg Bradley's Underground Gallery at the Yorkshire Sculpture Park in Wakefield.
This year's other entries range from a £33 million national museum charting the industrial heritage of Wales to a new gallery run by volunteers at a Medieval abbey in Oxfordshire.
The other schemes on the list are:
The Hunterian Museum, London - a series of new galleries showcasing some of the oldest medical collections in the world, designed by Julian Bicknell Associates;
The National Waterfront Museum, Swansea - a museum celebrating the country's industry and innovation, designed by Wilkinson Eyre;
The Concorde Experience, Museum of Flight, near Edinburgh - a £2 million museum redevelopment;
The Cambridge & County Folk Museum - a redevelopment of a local folk museum in Cambridge;
The Churchill Museum & Cabinet War Rooms, London - a new museum dedicated to the life and times of the wartime prime minister;
Dorchester Abbey Museum, in Oxfordshire - a collection of Medieval stones telling the 1,400-year story of the abbey;
The Collection: Art & Archaeology in Lincolnshire, Lincoln - a new museum displaying fine arts and artefacts; and
SS Great Britain, Bristol - Brunel's great ship preserved for future generations.
Chair of the 2006 judges, broadcaster Robert Winston said: 'This year's long list shows how museums and galleries, large and small, throughout the country are continuing to innovate and explore the boundaries.
'We, the judges, face a thrilling, if difficult, task ahead of us as we visit them over the coming months.'
The four finalists will be announced in April.