While the GO Train week-end service from Toronto to Niagara Falls actually stop operating after Canadian Thanksgiving on October 12th, 2009, there is a GO bus that will take you to Niagara Falls - the catch you have to take the GO train to Burlington to connect with the GO bus to Niagara Falls.
I'm not sure if the special GO train week-end service will be reinstated next year, but anyways, here's the schedule for the GO bus to Niagara Falls from Burlington: http://www.gotransit.com/publicroot/en/s…
As the other poster states, there is a VIA train to Niagara Falls, but it's more cost-prohibitive than the GO bus.

