Breweries
I'd definitely make an effort to go to Mill St. I went on a tour a couple years ago. You had to book in advance, but that meant it was a small group, and it was led by the brewmaster. I really like their Tankhouse Ale, and they produce a lot of other good/interesting beers, some of them only available at the brewery bar.
I'm also fond of the Heritage Brewery/Scotch-Irish beers (Sgt. Major's IPA, Corporal Punishment Brown Ale.) They're brewed in the Ottawa Valley, but you can often find them in good beer bars in Toronto.
Steamwhistle make a decent Pilsner, and the building the brewery is located in is pretty cool. I wouldn't go out of my way for a visit, but it's pretty central, so if you're nearby it wouldn't hurt.
The Amsterdam Brewery near King and Bathurst (I think they moved recently, but are still near the original location) is hit and miss, though I do like their Framboise.
Bars/Brewpubs
+1 for C'est What, Smokeless Joe's and the Granite Brewery .
In addition, you might want to try Volo on Yonge St. near Wellesley. They always have a couple of hand pumps, and loads of stuff in bottles (though many of the highlights are hard to find American beers, so it might not be quite so exciting for you
)
The Esplanade Bier Markt has a big selection, especially of Belgians, but it's crowded and often noisy, and I'd much sooner go to Smokeless Joe's or C'est What. They do make very good mussels there though. And if you're looking for a big night out with good beer, but also with dancing and a party crowd, it might be just what you're after.
The Cloak and Dagger is a really cozy place on College just west of Spadina. It has a great beer selection (10 or 15 taps with Canadian craft beers) and a wonderful atmosphere.
An old favourite of mine is the Bow and Arrow at Yonge and Davisville. A good (though not great) selection of Canadian craft brews, and some of the best pub food anywhere.
These places are all in Toronto proper. Afraid I can't offer too much info on Hamilton, but hopefully these help