The Canada Foundation for Innovation (CFI) (http://www.innovation.ca/index.cfm) provides funding mostly for infrastructure (e.g., large equipment, etc.)
the Networks of Centres of Excellence (NCE) (http://www.nce-rce.gc.ca/index.htm) funds partnerships between university, government and industry
Microsoft has a fellowship program for new faculty (http://research.microsoft.com/ur/us/nff/) for $100,000 a year for 2 years. It's open to US and Canadian faculty members. The ligibility requirements are as of the application year you must:
be in your first, second, or third year as a faculty member
be in your first faculty position
be no more than 6 years from the completion of your most recent PhD
Can be made to international students, but some students (e.g., those coming directly from mainland China) may be ineligible based on the systems that their transcripts use
Canadian students who apply must also apply for NSERC fellowships (see above)