Free and Open Source ecological software
Intro to R
Here are some pages that go through the basics of R programming.
Materials from an R workshop for ecologists developed by members of the New Zealand Ecological Society.
Intro material from Software carpentry on git-hub Read more about Software carpentry and their mission to teach lab skills for scientific computing.
R labs for (vegetation) ecologists by the Laboratory for Dynamic Synthetic Vegephenomenology at Montana State University. The site includes an introduction on the basics of R programming
Resources from Ben Bolker's book "Ecological Models and Data in R" are available from this website and the book's very own wiki.
The quick R wiki is a website created for both current R users, and experienced users of other statistical packages (e.g., SAS, SPSS, Stata) who would like to transition to R. The goal of the website is to help you quickly access this language in your work.
The R task views are a good starting point for finding a relevant package and function to carry out tasks spanning from "Bayesian inference" to "Time series analysis". There are currently 33 R task views.
Even though the R software is all about being open source most of the books about R are not free. From this website you can find a list of 147 for-purchase books relating to R.
vegan - Ordination methods, diversity analysis and other functions for community and vegetation ecologists.
ggplot2 - Powerful graphics package for both exploratory data analysis and publication quality figures.
LeafArea - An interface for the image processing program ImageJ, which allows a rapid digital image analysis for particle sizes.
igraph is a package for complex graph analysis, which implements useful metrics of centrality, and has great visualization capacities. 
bipartite is designed specifically for two-mode (predator–preys, parasites–hosts, pollinators–plants) networks. It implements most of the metrics used in the food web literature, and has really powerful null models simulators built in. 
network is a package to create and modify network objects. 
GFOSS-JRC and Spatial-ecology.net are wikis to help people learning open source tools for spatial analysis, modelling and data processing. You will find scripts and links for performing basic and advanced GIS operations in GRASS GIS, AWK, BASH, PKtools, R, GDAL, etc.
Docker is an open platform for developers to build, ship, and run applications under linux environments. Docker images that are ready for performing Geospatial Analysis, such as this ubuntu image can be useful tools for ecologists for easily running or embedding code or applications requiring specific linux environment under any OS.