Biomapper is a free GIS-toolkit to model habitat suitability
With C-Plan you can calculate the relative contribution (Irreplaceability and other measures) of land areas (sites) towards a predefined conservation goal
FloraMap predicts areas particular species might occur on the basis of previous observations and climate data
GARP predicts wild species distributions
More good software links at digitalgrove. Check out fGIS for shapefile editing.
Cartographic Links for Botanists (perhaps too dated now)
Managing genetic resources with GIS (from IPGRI/Americas)
Learn more about GIS
Do you find it difficult to get the right colors for your map?
Society for Conservation GIS