anybody know when do graduate student semesters end? do they end in april as well?

Don't grad students go year-round?
This info is probably on the registrar's website and may be dependent on the specific program, but I know most grad students are also in school in the summer - they get summer bus passes as well as Sept-Apr.

Here are the grad studies sessional dates: http://graduate.mcmaster.ca/images/S...calog_ACMS.pdf

When the department says the deadline for a masters program application is end of march, does that mean it's for people who start in may, or for people who start in september?

Kinda-sorta both. It's actually inclusive of the September start, but departments can make things happen for some applicants (in engineering at least...)