Here is a list of useful tools and open source software for conservation and ecosystem service projects that we have found. Let us know if you can add more!

InVEST is family of models to explore ecosystem service benefits and tradeoffs between spatial planning scenarios at a regional scale.

Open Data Kit (ODK) is a set of tools which help organizations author, field, and manage mobile data collection solutions. ODK provides an out-of-the-box solution for users to: Build a survey, collect and aggregate data on a server

QGIS is a cross-platform free and opensource desktop geographic information system (GIS).

R is a free, integrated suite of software facilities for data manipulation, calculation and graphical display.