Toronto's original 1910 subway plan. Some of the routes were kind of stupid, but nonetheless it would have been nice to have had a 40 year head start on subway construction.
A 1982 GO Transit plan to have high-speed, high-frequency, driver-less light metro service from Hamilton to Oshawa. Electrified trains and metro-like service are now only finally on the way.
The Guild Hall, proposed in 1834 on King Street.
A 1923 proposal for a monumental square across from Union Station. What
we got instead was arguably better, but it also could have been built elsewhere.
Like most cities, Toronto saw a whole bunch of planned towers cancelled after 1929. Maybe about half of these were ever completed.
More recently there was the massive Oxford Place casino + office + hotel + convention centre development, which was cancelled when the city rejected the casino. The office + convention centre portion is still in the works, but now on a delayed timeline and likely at a smaller scale.