Shane just turned Michelle Koo and on to this software package: The Software for Assisted Habitat Modeling for VisTrails. It seems very useful for a generalized SDM workflow.
From their blurb: The Software for Assisted Habitat Modeling for VisTrails has been created to both expedite habitat suitability modeling and help maintain a record of the various input data, pre- and post- processing steps, and modeling options incorporated in the construction of a species distribution model. SAHM is constructed as a "package" of modules that can be used within VisTrails, an open-source management and scientific workflow system designed to integrate the best of scientific workflow and scientific visualization systems. SAHM works by combining environmental predictor layers of the study area — such as climate and remote sensing data — with field sampling measurements for a particular species. The program then runs statistical models using these data to analyze habitat requirements of the species of interest and predict its potential distribution based on habitat suitability. Model outputs help land and natural resource managers generate maps to aid in predicting and managing species of concern.