For GO Transit and VIA Rail, Toronto's Union Station is the best place to start. While you can't see the tracks from inside the station there is a glass enclosed pedestrian walkway over the tracks called "The Skywalk" that goes from the west end of Union Station to the base of the CN Tower and Rogers Centre (formerly SkyDome). While you might get hassled if you hang out inside the Skywalk too long to take pictures and the dirty glass makes photography difficult, there should be no problems once just outside. Roundhouse Park is just steps south of there where the former CPR John Street roundhouse is located which houses the Toronto Railway Museum. The Museum is only open on weekends but there are still things to see outside when it's closed. There are also outdoor walkways over the tracks at either end of Rogers Centre.
The Bathurst St. and Spadina Ave. bridges are also good spots to catch the same action although the GO Bathurst St. Yard there has been decomissioned and may have been torn up. You could also go a few blocks further west to Strachan Ave. where the GO Milton, Georgetown, and Barrie lines and a few VIA trains all cross at street level.
A little further west, south of Queen St. at Roncesvalles Ave., there is another footbridge over the tracks and popular photo spot which goes to Sunnyside Park on the shores of Lake Ontario. You can get there by taking either the 501 Queen or 504 King streetcars. The Islington Avenue overpass which goes high above both GO's Willowbrook and VIA's Mimico yards is also a great photo spot.
While the Don Valley is certainly scenic there is little in the way of train traffic there except for a few Richmond Hill GO trains, the ONR Northlander, and VIA's three-times-a-week eastbound Canadian. The CPR line up the Don Valley hasn't been used in years.
There is very little in the way of freight in downtown these days as CN usually only operates one or two locals there each day and the CPR usually only works there at night. The main CPR route is in the northern part of the city which can be viewed from many spots. The main CP yard is a good place to go with road overpasses on Markham Road and Finch Avenue and the main entrance on McCowan Ave. CP's Lambton Yard, along Dundas St. around Runnymede Ave. is also a good choice.
For CN action you pretty much have to go outside Toronto. The best choices are by taking the GO Lakeshore line east to Pickering, Ajax, or Oshawa, or going west to Aldershot. Oshawa and Aldershot are also served by VIA if you want to travel in style and pay a lot more for the privilege. If you're lucky you might be able to catch the Ontario Southland Railway switching the plant at the Clarkson GO station and if you're really lucky they may be using an Alco RS instead of their usual Geeps.
Ken V. Moderator: Most things Canadian.
Any time could be train time!