I agree too the Waterfront Trail's (www.waterfronttrail.org) really nice, Prince Edward county too (did them in June).

Another area that's nice is Northumberland county, basically between Newcastle and Brighton (on Lake Ontario) north to Rice Lake; hilly and very scenic. Also in that area is Ganaraska Forest Outdoor Centre which is great for mountain biking.

Then there's Manitoulin Island. I've been there 4 times and enjoyed it very much (obviously!). Towns and villages are a bit far apart, especially on the west end. The roads are generally pretty quiet, except maybe for Hwy 6, with the ferry traffic. Mostly flat to rolling with a few big climbs in the north central area. There's a good hiking trail there too, called the Cup and Saucer Lookout Trail.

'Cottage Country' or Muskoka, an hour or so drive north of Toronto, is good place for riding, but be careful with traffic on weekends.

There are a number of nice rail trails too; Georgian trail, Cataraqui, Prescott-Russell, Hastings-Heritage, Victorian-Haliburton, Seguin, Midland Waterfront, Caledon, and a few others that are probably more suited for MTBs.