Several ecosystem services are provided by farming systems. These include climate regulation (i.e. greenhouse gases), food production, nutrient cycling, organic matter decomposition and dynamics, water protection etc. There are standard methods that can be used in assessing each of these services. for example, for climate regulation, greenhouse gases of concern like carbon dioxide, methane and nitrous oxide can be measured.
I'm afraid that the answear is NO. There is not a standard methodology for ESs assessment. As Kobby said there are many standards techinique to assess ONE ES at the time, however few resesches seems to have a multiscale and multidisciplinary approach as suggested by the Millennium Ecosystem Assessment.