Good books on modeling

Otto & Day: A Biologist's Guide to Mathematical Modeling in Ecology and Evolution
Railsback & Grimm: A Course in Individual- and Agent-based Modeling
Nowak: Evolutionary Dynamics: Exploring the Equations of Life
Grimm & Railsback: Individual-based Modeling and Ecology

Relevant societies and groups (general / speciation)

AAAS: American Association for the Advancement of Science
ASN: American Society of Naturalists
CSEE: Canadian Society for Ecology and Evolution
FroSpects: Frontiers of Speciation Research (a European Research Networking Programme)
LERN: London Evolutionary Research Network
SSE: Society for the Study of Evolution
UK Speciation Group (which needs an acronym, obviously; UKSG?)

Relevant societies and groups (modeling / mathematical biology)

SIGEVO: ACM Special Interest Group on Genetic and Evolutionary Computation
CAMBAM: Centre for Applied Mathematics in Bioscience and Medicine
IIASA EEP: The Evolution and Ecology Program at the International Institute for Applied Systems Analysis
ISEM: International Society for Ecological Modeling
MBI: Mathematical Biosciences Institute

Software

BOINC: a distributed computing platform
Nemo: a software platform for building spatially explicit individual-based genetic models
NetLogo: a language/environment for constructing individual-based simulations
R: a language/environment for statistical computing and graphics
Sun Grid Environment (SGE): a cluster computing platform
Also, Xavier Thibert-Plante has a list of some other useful software

Graduate school tips & advice

How to write a paper in scientific journal style and format
PhD comics
Some modest advice for graduate students
The importance of stupidity in scientific research
Tomorrow's professor

Other good stuff

Cloud Appreciation Society
Complexification
Mr. Deity
Oxidizer
Pharyngula
simbiotic software
Union of Concerned Scientists
xkcd