~ Software applications

Productivity
Source Forge massive collection of open-source software apps
OpenOffice open-source productivity software, compatible with Microsoft Office files
PDFsam handy and free little app for splitting and merging PDFs
VLC multimedia player excellent media player

Ecological modeling

Ecology Software Clearinghouse Deihl and Larkin, University of Illinois Natural History Survey
EcoSim community ecological modeling, Entsminger and Gotelli

EcoTools open-source ecological modeling, Entsminger and Gotelli
Netica development of Bayesian network models
OpenBUGS open-source software for fitting Bayesian models
PopTools Microsoft Excel extension for demographic modeling, CSIRO, Australia

Patuxent Software Archive software for analysis of ecological data, USGS Patuxent Wildlife Research Center
Program DISTANCE Research Unit for Wildlife Population Assessment
Program MARK Gary White, Colorado State University
Program PRESENCE Daryll MacKenzie,
USGS Patuxent Wildlife Research Center
WinBUGS software for fitting Bayesian models
WINE open-source application for running Windows software on Mac OS X
Vortex population viability analysis, B. Lacey

R free and open-source statistics software
AICcmodavg model selection with information criteria, and model averaging, M. Mazerolle.
glmulti model selection with information criteria, V. Calcagno
lme4 generalized linear mixed-effects models, D. Bates and M. Maechler
popbio matrix models of population growth, sensitivity, and elasticity, C. Stubben, B. Milligan, and P. Nantel
R CRAN source for most R packages
unmarked model occupancy, abundance, density, and other parameters with count data from unmarked animals, I. Fiske, R. Chandler, and J. Royle

Geospatial
Garmin Application down/uploads GPS data, Minnesota Department of Natural Resources
Geospatial Modelling Environment ArcMap extension with user-friendly geospatial tools, Hawthorne Beyer
Hawth's Analysis Tools ArcMap extension with user-friendly geospatial tools, Hawthorne Beyer
Magnetic Declination Computer estimates magnetic compass declination, NOAA
Open source GIS:
GRASS
gvSIG
Quantum GIS