If you are looking for an Applied Physics (or Engineering Physics) graduate program in Canada, then you are looking for a "Masters of Applied Science" (MASc) degree, not a Masters of Science (MSc) degree. So if you are not finding the right program, then you might be looking in the wrong place! For your interest, you might also want to look at "Material Science" programs, not just Engineering Physics / Applied Physics programs. Note that in most schools, the "Applied Physics" program is connected with the Department of Physics while Material Science is more connected to engineering oriented departments.
Note: some schools call their "MASc" degree a "MEng" degree instead (Masters of Engineering). If a school offers both, then usually the MEng degrees are more professional and usually have more courses and less research while a MASc would be more research oriented. But if there is only one choice, then they are often the same thing, just a different name.
In Canada, the general route to get to a MASc/MEng program is by first getting a BASc or some equivalent undergrad engineering degree, but this is not required. Usually though, for a MASc in Applied Physics, they would prefer a BASc in Engineering Physics but not all schools have as strict as a requirement. The higher ranked the school, the pickier they are, as expected.
I would say that a MASc/MEng degree is meant for those who want to be trained as an engineer and work on engineering problems, while a student that wants to be trained as a physicist and work on problems in the intersection of engineering and physics should go for a Physics MSc. To me, it sounds like you have a better background and more research fit with a MASc/MEng program, but this is based on the very limited information I know about you!
In general, the PGRE is not usually required for graduate programs in Canada. However, some schools do recommend (and in a few cases, require) the PGRE for international applicants. I would guess that Applied Physics programs will care less about the PGRE than "pure" Physics programs.
Oh, finally, here is an example of a MASc program in Engineering Physics in Canada: http://www.phas.ubc.ca/graduate-program ... e-students
(this is a top school in Canada and note that an undergrad engineering degree in Electrical Engineering is an acceptable pre-req for a MASc in Engineering Physics here).