Canadian parks that offer backcountry camping.

Alberta 

Banff National Park
http://www.pc.gc.ca/eng/pn-np/ab/banff/index.aspx

Elk Island National Park
http://www.pc.gc.ca/eng/pn-np/ab/elkisland/index.aspx

Jasper National Park
http://www.pc.gc.ca/eng/pn-np/ab/jasper/index.aspx

Waterton Lakes National Park
http://www.pc.gc.ca/eng/pn-np/ab/waterton/index.aspx

Wood Buffalo National Park
http://www.pc.gc.ca/eng/pn-np/nt/woodbuffalo/index.aspx

Peter Lougheed Provincial Park
http://www.albertaparks.ca/siteinformation.aspx?id=307

Spray Valley Provincial Park
http://www.albertaparks.ca/siteinformation.aspx?id=308

The province of Alberta, has numerous other Provincial Recreation Parks, Wildland Parks and Natural Areas that offer backcountry camping, and are managed by Alberta Parks. Information can be found here...
http://www.albertaparks.ca/searchparks.aspx

British Columbia

Glacial National Park
http://www.pc.gc.ca/eng/pn-np/bc/glacier/index.aspx

Kootenay National Park
http://www.pc.gc.ca/eng/pn-np/bc/kootenay/index.aspx

Mt. Revelstoke National Park
http://www.pc.gc.ca/eng/pn-np/bc/revelstoke/index.aspx

British Columbia has one of the largest park systems in the world for backcountry camping, I won't list them all, well over 200.
Information can be easily found here...
http://www.env.gov.bc.ca/bcparks/explore/

Manitoba

Riding Mountain National Park
http://www.pc.gc.ca/eng/pn-np/mb/riding/index.aspx

Wapusk National Park
http://www.pc.gc.ca/eng/pn-np/mb/wapusk/index.aspx

Atikaki Provincial Wilderness Park
http://www.gov.mb.ca/conservation/parks/popular_parks/eastern/atikaki_info.html

Bakers Narrows Provincial Park
http://www.gov.mb.ca/conservation/parks/popular_parks/northwest/bakers.html

Clearwater Lake Provincial Park
http://www.gov.mb.ca/conservation/parks/popular_parks/northwest/clearwater.html

Duck Mountain Provincial Park
http://www.gov.mb.ca/conservation/parks/popular_parks/western/duck_info.html

Grass River Provincial Park
http://www.gov.mb.ca/conservation/parks/popular_parks/northwest/grass.html

Nopiming Provincial Park
http://www.gov.mb.ca/conservation/parks/popular_parks/eastern/nopiming_info.html

Spruce Woods Provincial Park
http://www.gov.mb.ca/conservation/parks/popular_parks/western/spruce.html

Turtle Mountain Provincial Park
http://www.gov.mb.ca/conservation/parks/popular_parks/western/turtle_info.html

Whiteshell Provincial Park
http://www.gov.mb.ca/conservation/parks/popular_parks/eastern/whiteshell_info.html

New Brunswick

Fundy National Park
http://www.pc.gc.ca/eng/pn-np/nb/fundy/index.aspx

Kouchibouguac National Park
http://www.pc.gc.ca/eng/pn-np/nb/kouchibouguac/index.aspx

Newfoundland & Labrador

Gros Morne National Park
http://www.pc.gc.ca/eng/pn-np/nl/grosmorne/index.aspx

Terra Nova National Park
http://www.pc.gc.ca/eng/pn-np/nl/terranova/index.aspx

Barachois Pond Provincial Park
http://www.env.gov.nl.ca/env/parks/parks/p_bp/index.html

International Appalachian Trail Newfoundland & Labrador
http://www.iatnl.ca/index.php/our-trail/blow-me-down-mountain-trail/

Nova Scotia

Cape Breton Highlands National Park
http://www.pc.gc.ca/eng/pn-np/ns/cbreton/index.aspx

Kejimkujik National Park
http://www.pc.gc.ca/eng/pn-np/ns/kejimkujik/index.aspx

Northwest Territory

Aulavik National Park
http://www.pc.gc.ca/eng/pn-np/nt/aulavik/index.aspx

Nahanni Reserve National Park
http://www.pc.gc.ca/eng/pn-np/nt/nahanni/index.aspx

Tuktut Nogait National Park
http://www.pc.gc.ca/eng/pn-np/nt/tuktutnogait/index.aspx

Northwest Territory Parks & Trails
http://www.nwtparks.ca/

Nunavut

Auyuittuq National Park
http://www.pc.gc.ca/eng/pn-np/nu/auyuittuq/index.aspx

Sirmilik National Park
http://www.pc.gc.ca/eng/pn-np/nu/sirmilik/index.aspx

Ukkusiksalik National Park
http://www.pc.gc.ca/eng/pn-np/nu/ukkusiksalik/index.aspx

Ontario

Ontario has more than 6,500 backcountry campsites - accessible only by canoe or on foot.

Bruce Peninsula National Park
http://www.pc.gc.ca/eng/pn-np/on/bruce/index.aspx

Georgian Bay Islands National Park
http://www.pc.gc.ca/eng/pn-np/on/georg/index.aspx

Pukaskwa National Park
http://www.pc.gc.ca/eng/pn-np/on/pukaskwa/index.aspx

St. Lawrence Islands National Park
http://www.pc.gc.ca/eng/pn-np/on/lawren/index.aspx

Algonquin Provincial Park                                                                    The Friends of Algonquin Park
http://www.ontarioparks.com/english/algo.html                                        http://www.algonquinpark.on.ca/

Algonquin Park Map
http://www.algonquinmap.com/

Bon Echo Provincial Park
http://www.ontarioparks.com/english/bone.html

French River Provincial Park
http://www.ontarioparks.com/english/fren.html

Frontenac Provincial Park                                                                    The Friends of Frontenac PP
http://www.ontarioparks.com/english/fron.html                                        http://www.frontenacpark.ca/              

Grundy Lake Provincial Park
http://www.ontarioparks.com/english/grun.html

Killarney Provincial Park                                                                       The Friends of Killarney Park
http://www.ontarioparks.com/english/kill.html                                           http://www.friendsofkillarneypark.ca/

Quebec

Forillon National Park
http://www.pc.gc.ca/eng/pn-np/qc/forillon/index.aspx

La Mauricie National Park
http://www.pc.gc.ca/eng/pn-np/qc/mauricie/index.aspx

Mingan Archipelago National Park Reserve
http://www.pc.gc.ca/eng/pn-np/qc/mingan/activ.aspx

Parc National d'Aiguebelle
http://www.sepaq.com/pq/aig/

Parc National du Bic
http://www.sepaq.com/pq/bic/

Parc National de Frontenac
http://www.sepaq.com/pq/fro/

Parc National de la Gaspesie
http://www.sepaq.com/pq/gas/

Parc National des Isle de Boucherville
http://www.sepaq.com/pq/bou/

Parc National de la Jaques Cartier
http://www.sepaq.com/pq/jac/

Parc National du Mont Megantic
http://www.sepaq.com/pq/mme/

Parc National du Mont Orford
http://www.sepaq.com/pq/mor/

Parc National des Monts Valin
http://www.sepaq.com/pq/mva/

Parc National du Saguenay
http://www.sepaq.com/pq/sag/

Saskatchewan

Grasslands National Park
http://www.pc.gc.ca/eng/pn-np/sk/grasslands/index.aspx

Prince Albert National Park
http://www.pc.gc.ca/eng/pn-np/sk/princealbert/index.aspx

Athabasca Sand Dunes
http://www.tpcs.gov.sk.ca/AthabascaSandDunes

Clarence-Steepbank Lakes Provincial Park
http://www.tpcs.gov.sk.ca/Clarence-SteepbankLakes

Clearwater River Provincial Park
http://www.tpcs.gov.sk.ca/ClearwaterRiver

Lac La Ronge Provincial Park
http://www.tpcs.gov.sk.ca/LacLaRonge

Narrow Hills Provincial Park
http://www.tpcs.gov.sk.ca/NarrowHills

Yukon

Tombstone Territorial Park
http://www.env.gov.yk.ca/parksconservation/tombstonepark.php

Herschel Island Qikiqtaruk Territorial Patk
http://www.env.gov.yk.ca/parksconservation/HerschelIslandQikiqtaruk.php