The Basics:

Transport Canada 
Kaysam Balloons 
Helium, High Pressure Tank Safety 
Balloon Launch FAQ 

Online References:

Weather Sounding Data for North America 
CRWS Jet Stream Map Menu 

MISRA C - Guidelines for using the C language in safety-related systems 
WWW Virtual Library for Safety-Critical Systems 
Ed Williams' Aviation Navigation Equations page 
Geometry Formulas and Facts 
Simon Kapadia - Quickcam Interfacing
Richard Nakka's Parachute Design and Construction

Books:

Safer C - Developing Software for High-Integrity and Safety-Critical Systems 
Model Aircraft Aerodynamics, by Martin Simons 
Flight Stability and Automatic Control, by Robert C. Nelson
Fundamentals of Aerodynamics, Second Edition 
Practical Reliability Engineering, Third Edition

Some major parts suppliers:

YAM packet modem 
Tekk Data Radio 
Garmin - OEM and consumer GPS manufacturer 
Precision Navigation's Vector 2x Compass Module
Tokin Ceramic Gyros 
Analog Devices - Accelerometers 
PC-104 Vendors 
Digi-Key Mail-Order Electronic Components

Locally, these two shops have also been a great help:

Muir Communications  
Queale Electronics

A good directory of balloon projects of all kinds:

AMSAT and High Altitude Balloons 

Other amateur balloon groups whose sites have been helpful:

University of North Dakota High Altitude Balloon Project 
Near Space Balloon Group 
Edge of Space Sciences 
Vernon Balloon Experiments 
Bear - Edmonton

And, another balloon / glider project in Academia:

Glidersonde Demonstrator Program