Inexpensive lodging across Canada
 

Travelling across Canada by car and would like inexpensive, clean, comfortable, no frills nightly lodging.

If you could provide more information, you'll get more assistance. Are you planning to stop in major cities? What sort of route are you planning to take? Are you planning the whole trip and reserving in advance or is your itinerary flexible? What time of year are you planning to travel? And what's inexpensive to you?
Generally, there aren't as many motel/hotel chains in Canada as there are in the US. So while people can recommend a chain, it's not likely that you'll find one of their properties every place you plan to stop. Best Western is probably the most commonly found chain here.

If your travels take you to Jasper, Alberta (Jasper National Park in the Canadian Rockies), you might be interested in "private home accommodations" - rooms or suites in a resident's home. Some of the more basic ones are as low as $55 or $60 a night, with no additional taxes (which saves you further 11% over hotel rates).

What about hostels http://www.hostelcanada.com/; http://www.hihostels.ca/

Or Bed and Breakfast lodging's --
http://www.bbcanada.com/