One thing that has always been on my to-do list in Toronto, but I have yet to do is go to a comedy show at Second City. It's walking distance from Union Station. My brother and sister-in-law went and said it was great.
I always love going to see live theater in Toronto - there are three or four theatres with Broadway shows, all within walking distance and mirvish.com would have what is playing for all of them.
I haven't been to the Aquarium, but my friend who travels a lot highly recommends it. I was meh on the CN Tower personally. I finally went because I'd been to Toronto 10 or 11 times without doing the CN Tower and figured I should finally do it but it wasn't anything special and I felt like it was overpriced.
If you are into fine dining and don't mind spending a lot on a fancy meal, Canoe is probably the most upscale restaurant I've been to in Toronto. It's on the 60th floor so has a great view of Lake Ontario.
For more casual meals - I had a fun meal at the Sultan's Tent & Café, a Moroccan restaurant with belly dancers. Amsterdam Brewhouse is right on the water - they had good food and drinks. I also liked the Loose Moose and Beerbistro.