I strongly recommenced picking a potential supervisor rather than a potential university.

Another thing you should do is apply for funding/scholarships.

Personally, I don't recommend skipping the Masters though.

Finally, you should be sure this is something you want to do. Graduate degrees are not always a wise investment and in many cases you will never recoup money that could have been made if you had just gone right into work in industry (you might make a higher starting salary but will be at least 2 years behind in experience). I would only recommend it if you want a more research focused job or to go on to a PhD and then academia (risky as there are few jobs right now).

If there is a professor at Guelph doing research you are interested in and you already have a relationship with him why not consider going there? Who your supervisor is, what research you are doing and your publication record are far more important than what school you are going to (assuming it is accredited). I strongly recommenced picking a potential supervisor rather than a potential university. Not all faculties will have members doing research in all areas, so it is important to find a department with a research group (or at least a professor) doing research you are interested in.

Now to address your question. The best thing you can do to increase your admission chances for grad school is to have a potential supervisor lined up before hand. You should be meeting with potential supervisors and discussing working with them, your research interests, etc. In many cases supervising faculty members have a large say in graduate admissions and having one that wants to work with you would go a long way to being accepted.

Another thing you should do is apply for funding/scholarships. You can do this before you are accepted and being funded makes you a far more attractive prospect to potential supervisors. I believe that the NSERC deadline has past for next year, but you can probably still apply for OGS (each University has a different deadline and application process for OGS now so it will depend on where you are applying).

When you say that "I took 2 graduate courses already, in which I wrote 2 papers", do you mean you published those papers? If they were published in a peer reviewed conference or journal this could help significantly. Be sure to mention this in your application and to potential supervisors.

Your cumulative average sounds great, but grades are less important for graduate applications (assuming they are over the minimum and would not make you ineligible for funding/scholarships) then for undergrad. Most departments also have their own method of calculating your grade (for example some only consider 4th year courses, your last X number of credits, courses taken in your last Y years, etc.)

Most graduate applications have a statement of purpose section that you should put some work into. There are many resources you can find on Google to help you with this but you should at a minimum have someone read it over for you.

You will also likely need at least two references. These should be professors you have worked with and trust to give you a strong recommendation. Make sure they actually complete and submit the reference form on time (you don't want your application thrown out because your reference forgot to submit their part).

Are you applying for Masters or trying to jump right into a PhD? If you are applying for a Masters I would say your odds are good if you talk to a potential supervisor before hand. PhD might be more difficult as you will be competing with applicants with Masters degrees and publication records. If you do want to skip the Masters it may be a better idea to apply for a Masters and then switch to PhD after a year or two (depending on what the departments regulations are). Personally, I don't recommend skipping the Masters though.

Finally, you should be sure this is something you want to do. Graduate degrees are not always a wise investment and in many cases you will never recoup money that could have been made if you had just gone right into work in industry (you might make a higher starting salary but will be at least 2 years behind in experience). I would only recommend it if you want a more research focused job or to go on to a PhD and then academia (risky as there are few jobs right now).

Edit: Also I should point out that sadly the theory fields in CS are not exactly the most popular right now. While this should not stop you from pursuing your interests, it does mean it will be harder to get published, get funding and later a job if it is the sole focus of your research. The big areas right now are Big Data (and Data Analytics), Cloud Computing, eHealth, Machine Learning (mostly Computer Vision) and Bioinformatics. If you can some how involve one of those into your research, it will make your life easier.

Well in recent years the PhD program at Guelph got totally cancelled because the students they were graduating knew next to nothing. They only recently brought it back and it isn't even a computer science PhD you'd be getting, you would have to do an interdisciplinary PhD.

On the topic of good fields to be in, is Computer Security a good field? Personally I really like the theoretical computer science, and find a lot of the fields you listed as kind of boring, with the exception of machine learning.

I was thinking of finishing a PhD and going into academia in the long run. Another question is, what are some of the things people look for when hiring you in academia?

My professor also suggested that I finish a Masters before PhD because a PhD isn't for everyone and it's better to waste 2 years of your time than 3-4.

Anyway, since I know this is anecdotal so it shouldn't be taken as fact, but all of the professors I know at my University that are in a theoretical field have no problems getting published, actually they publish the most papers.

Also, the fields you specified seem over saturated to me, in my school the professors that take students under these fields have something like 10-15 students.

One of the arguments my professor made for going to graduate school is that, as undergraduate students we are already used to being poor, so being poor for a few more years shouldn't be a problem (hahaha).

About the NSERC scholarship, my professor thinks I am a good candidate so he is trying to prepare me as much as he can for when you need to apply.

Also another thing about graduate school in general, does your degree have more to do about what school you went to or what advisor you had? I know I don't want to be at Guelph for a PhD but then what should I aim for, Waterloo or Toronto, or somewhere else with a "better" advisor?