Update 2017/7/1: This is the most linked-to post of [Alon Levy’s] about construction costs, even though the dataset here is relatively small. You can see links to more posts, with more datapoints, on his static construction cost page. The long and the short of it is that in non-English-speaking developed countries, the typical range for urban subways is $100-300 million per km, with a few outliers in both directions.
East Side Access: $8.4 billion; excluding pre-existing tunnels, this consists of 2 km of new tunnel in Manhattan and a new connection in Queens. So this is about $4 billion per km.
Second Avenue Subway Phase 1: $4.9-5.7 billion in 2007-17 for about 3 km of new tunnel. This is $1.7 billion per km.
NYC 7 Line Extension: $2.1 billion in 2007-12 for 1.6 km of new tunnel. Note that this has only one station, an unusually sparse spacing for a dense urban area. This is $1.3 billion per km.
Crossrail: £15 billion in 2008-18 for a line of more than 100 km, of which the primary component is 22 km of new tunnel under Central London and Heathrow Airport. Due to the extensiveness of the London Underground network, this is the most complex project on the list. The cost per unit of tunnel is about $1 billion per km, making this the only outside New York to cross the $1 billion line.
Central Subway: $1.58 billion in 2010-6 for 2.7 km of light rail tunnel. This project is only on this list because it has to cross under the double-decked subway (Muni and BART) under Market; the standards, including station size, are for light rail. This is about $500 million per km.
Jubilee Line Extension: £3.5 billion in 1993-9 for 15.9 km of route, of which about 80% is underground. The line went over budget by 66%, crosses under the entire London Underground network, and crosses under the Thames four times. This is about $450 million per km.
Amsterdam North-South Line: €3.1 billion in 2009 money for 9.5 km of new tunnel. The project has run over budget by a factor of more than two, leading to accusations of boondoggle and remarks that the project should not have been built. This is $410 million per km.