I will ALWAYS recommend the Steam whistle brewery tour to anyone visiting Toronto. Love that brewery. Pay the price of a six pack. Get a beer while you wait. A beer at the start of the tour, a beer at the end of the tour, and a six pack to take home. Good deal.
It's right across from the Aquarium. Which is also a fun thing to d, but pricey. I'd recommend going mid day weekdays to avoid the crowds. Weekday nights after 7pm are also cheaper and on Fridays they often have events.
The AGO has a Banksy exhibit right now.
The ROM has an exhibit on spiders.
If you want to do all the touristy stuff get a citypass, it'll save you a bundle.
www.citypass.com/toronto.
Less touristy stuff:
Just For Laughs Festival is in town right now.
Toronto Beaches Festival this weekend.
Shameful Tiki Room, on Queen st.
If you're a Harry Potter fan you should check out Curiosa, also on Queen St. It is modelled after Diagon Alley.
I always recommend everyone check out Kensington Market. It's most fun on Pedestrian Sundays, but it sound like you won't be here for that (Sept 30th)
You also just missed Polish Fest on Roncesvalles (Toronto's Little Poland)
Always fun to check out both High Park, and Centre Island if you just want to have a nice day outside with some pretty scenery.