Canadian military records and artifacts reside in various places.
The Canadian Forces themselves have a small organization called the Directorate of History and Heritage (DHH - formerly known as the Directorate of History or DHist, a designation which you still see in notations).
http://www.cmp-cpm.forces.gc.ca/dhh-dhp/index-eng.asp
DHH writes official histories for the Canadian military and conducts various other related duties. They're a small staff of 20ish on the outskirts of Ottawa, some military, some civilian academics. If you surf around their site you will find pdf copies of official histories, and nifty scans of many field reports from their teams of official historians with the troops in WWII. You'll also find details on visiting their records (they have a public reading room) and requesting records from them.
Canadian military records tend to wind up at DHH first (in particular all of the war diaries from contemporary ops), and various other records are archived there, but in general, the final resting place for all Canadian military records is -- as for all Canadian federal records -- is Library and Archives Canada (LAC).
http://www.collectionscanada.gc.ca/mili ... dex-e.html
LAC's main building is right downtown in Ottawa, right on Parliament Hill. They too have public reading rooms, and details on their website about requesting records from them.
Very nearby in Ottawa is the Canadian War Museum (CWM).
http://www.warmuseum.ca/home/
The CWM too has records, even more artifacts, and a library open to the public.
Also, there are numerous other museums across the country with various records and artifacts of note, in particular:
The National Air Force Museum in Trenton, Ontario (home of one of Canada's largest and most historic air bases)
http://www.airforcemuseum.ca/
The Military Museums of Calgary (formerly the Museum of the Regiments)
http://themilitarymuseums.ca
The Maritime Museum of the Atlantic in Halifax is not specifically military, but includes much on that subject.
http://museum.gov.ns.ca/mmanew/en/home/default.aspx
Lastly, in terms of online resources, the government runs the Canadian Military History Gateway:
http://www.cmhg.gc.ca/flash/index-eng.asp