Finding a Canadian university that will waive its application fees is not an easy task. Although most colleges will grant a waiver to those who present a financial hardship, they don't wish to make it too easy and don't advertise that fact. After reviewing the application fee policies of the universities you're interested in, the best thing to do is to write directly to them to ask what's required to obtain an admissions fee waiver.
University of Toronto School of Law
If you're applying to universities within Ontario, you must apply through The Ontario Universities' Application Centre (OLSAS). The University of Toronto School of Law cannot waive the $110 application fee that goes to OLSAS for the processing of the application, but it is able to waive its own $90 fee if you complete the fee waiver form available on its website.
University of Calgary
Applicants to the Faculty of Medicine at the University of Calgary must pay all fees at the time of registration, but Canadian medical school residents who take electives at the university will have all fees waived on a reciprocal basis. The school offers a three-year doctor of medicine degree, as well as master's degrees in biomedical technology and community medicine, and a doctor of philosophy degree.
Canadian Virtual University
Several universities specializing in online and distance education are members of Canadian Virtual University (CVU). Students enrolled in courses offered by CVU members don't have to pay an application fee to take a course at another CVU school. They simply fill out a Letter of Permission/Visiting Form available on the CVU website. CVU-member universities are Athabasca University, Carleton University, Laurentian University, Memorial University of Newfoundland, Nipissing University, Royal Military College of Canada, Royal Roads University, TÉLUQ, l'université à distance de l'UQÀM, Thompson Rivers University, University of Manitoba, and University of New Brunswick.
The SATo Program
According to the College Board, there are no colleges in Canada that cooperate with the SATo Program, which waives application fees for students who've had their SAT application fees waived due to financial hardship. There is a “Canada College” on the list of SATo Program schools, but it's located in California.