From a UK perspective, there are two broad approaches towards PES.
The first is long established and linked to the EU's common agriculture policy - the stewardship schemes run by Natural England that reward farmers for following certain specified pro-biodiversity etc. practices. There is some on-going investigation towards expanding these schemes to encompass climate change mitigation. The existing scheme, in my opinion, lacks for robust data and farm audit process regarding the measurable impact of the ecosystem services created.
The second is a more recent private, voluntary programme that I've been involved in. Essentially I've been auditing large-scale, increasingly national-level farm carbon footprint measurement and management programmes - typically based around livestock. These are not linked (as yet) to payments, but do show what might be involved in running a cost-effective PES.
For a livestock mitigation programme, the extent of data required and achieving suitable quality of data is critical - particularly when budgets are small.
For an arable mitigation programme, the key factors for me are balancing yield against inputs. Anything which increases yield whilst maintaining or reducing the inputs required is a positive thing and can be measured quite cost effectively. I would include in this list soil improvement as part of a sequestration programme - I believe that any benefit from such a programme will create much more value, more simply, for the farmer via lower costs and increased yields from better soil than carbon credits or direct PES.
PES in my view are typically best targeted at research, capacity building and farmer engagement programmes that will enable them to generate win-win scenarios of better soil and lower emissions accompanied by increased production and profits.
Links and resources:
RPE/PES in the Agricultural and Food Sectors
Payment for Ecosystem Services and Food Security
Paying farmers for environmental services
FAO website on PES
Payments for environmental services - What role in sustainable agricultural development?
Climate Change Mitigation Finance for Smallholder Agriculture
Payment Schemes for Environmental Services in Watersheds
The new generation of watershed management programmes and projects
FAO's activities on watershed management and mountains