Transport Canada is the Canadian government department which regulates aviation in Canada.  NavCanada is the private corporation that runs Canada's air traffic control system. Also important if you're coming in to Canada from the US or Europe are the Canadian Border Services Agency regulations respecting customs. Below you'll find detailed links to useful areas on their sites.

Aircraft/flight crew/flight regulations:

The rules for aviation in Canada are contained in the CARS - Canadian Aviation Regulations.  See Part VI for operating and flight rules.  Of particular interest for trips north are the Sections 602.60/61/62/63 on Survival Equipment.

Transport Canada has special sections on its website for General Aviation and Civil Aviation. Both contain valuable information.

The Transport Canada Aeronautical Information Manual provides details about all aspects of flying for pilots in Canada, including licensing, registration, rules of the air, flight planning, meteorology, charts, communications, search and rescue and more.  The complete manual can be downloaded from the Transport Canada Website.

The Transport Canada Glossary for Pilots and Air Traffic Services is helpful if you're coming to Canada from elsewhere. It provides definitions for terms used in Canadian aviation, with explanations where those differ from FAA (US) and ICAO (international) terminology.

Transport Canada also publishes a quarterly free download-able Aviation Safety Newsletter, with interesting articles and lots to think about.

Flight plans, weather, traffic control and fees:

NavCanada is the private, non-share capital corporation which operates Canada's air navigation system. The fees associated with aircraft use in Canada pay for NavCanada's services.  Their website contains detailed places for aviation weather, flight planning and more.  NavCanada is introducing new flight plan requirments as part of the international implementation of ICAO flight plan content changes.  Below are a number of direct links to items of interest:

• to file a flight plan in Canada, call 1-866-WXBRIEF or 1-866-541-4109
• NavCanada Collaborative Flight Planning System for on line filing/amending/delaying/cancelling flight plans
• Aeronautical Information Publications (AIP Canada); Aeronautical Information Circulars;
• NavCanada on-line store for purchase of PDF versions of Canada Flight Supplement, CAP IFR approach plates/charts, VNC charts, and other publications.
• Northern and Aviation Weather info
  
• NOTAMS
• Canadian NOTAM Procedures Manual and revisions.
• Aeronautical Information Circulars
• Aviation Weather Services Guide includes info on differences between Canadian and US services
• Canadian Designated Airspace Handbook includes maps of Northern Domestic Airspace
• Guide to NavCanada fees
• Canadian Owners and Pilots Association information for general aviation in Canada.
• Foreflight now provides digital Canadian aviation charts for iPad

Canadian Flight Planning software

• World Flight Planner
• Flight Wizard

Online flight planning tools

• Fltpln.com US service has some Canadian airport information/charts/weather etc.
• Phone E6B provides a Blackberry/Android version of the venerable E6B flight calculator and more.
• CoPilot - general aviation flight Planning tool for iPhone and Palm

For airport information for Baffin Island communities, select COMMUNITIES on the menu at left, and choose the community. Airport informtion is available or each communitiy.

And don't forget, Canadian airspace is divided into two main regions - Southern Domestic Airspace, and Northern Domestic Airspace.  Most of Arctic Canada falls into Northern Domestic Airspace, except for a little bubble around Iqaluit and Kimmirut which remain in Southern Domestic Airspace.  In Northern Domestic Airspace, runway headings, tracks etc, are given in degrees TRUE, rather than magnetic, due to the great magnetic deviation when you get this far north.

And of course, this region is also the Standard Pressure Region for the purpose of altimeter settings.

For a detailed look at the historical development of flight navigation in the high arctic, check out this publication from the Royal Canadian Air Force in 1941.