If I wanted to go into Honours Chemistry (that program is NOT limited and I have the grade requirements for it), will I be able to get in even though I put Honours Chemistry as my third choice..
Will the fact that it is my third choice affect my acceptance?

I am pretty sure you are able to choose from any of the programs you are eligible to enter.

is there any way of getting into a program if you miss the pre-req by a small amount, i dont have the 6 average in chem :/

It depends. I know for engineering, I got into my first choice but all the others were crossed out when I was choosing my courses since the others were filled by then. Not sure if it is the same for science

Originally Posted by Danielrus

is there any way of getting into a program if you miss the pre-req by a small amount, i dont have the 6 average in chem :/

I think you'll be able to shadow the program. You can take almost all of the courses without actually being in chem (except for the lab courses, 2LA3 and 2LB3, but you can get waivers for them). Then, you can get your average up and transfer completely into the program after next year. I know someone who shadowed this year.