They use the price gap approach - which is the common methodology for consumption subsides.
The Price Gap Approach
The IEA estimates subsidies to fossil fuels that are consumed directly by end-users or consumed as inputs to electricity generation. The price-gap approach, the most commonly applied methodology for quantifying consumption subsidies, is used for this analysis. It compares average end-user prices paid by consumers with reference prices that correspond to the full cost of supply. The price gap is the amount by which an end-use price falls short of the reference price and its existence indicates the presence of a subsidy. In a given economy..
IEA - Methodology for Calculating Subsidies
So what methodology does the IMF use?
Subsidies for petroleum products are calculated for 176 countries using the price gap approach drawing on data compiled by IMF staff, the OECD, and Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ) for 2000–2011. Consumer subsidies are estimated for gasoline, diesel, and kerosene. Producer subsidies to refineries to cover inefficient operations are not estimated due to the lack of data. Therefore, our estimated petroleum product subsidies capture only consumer subsidies and should be seen as a lower bound. See Appendix I for details.
http://www.iea.org/media/weowebsite/factsheets/factsheets.pdf
http://www.imf.org/external/np/pp/eng/2013/012813.pdf
New Report Highlights Fossil-Fuel Exploration Subsidies in G7 Countries | Global Subsidies Initiative