Woodfire Bagels has good, smoky, Montreal-style bagels. Enough said. Get there earlier if you want them hot. Open Monday to Saturday, 8am to 5pm (or until the bagels run out). (Near Fairview Mall in Kitchener, see map. Some 7 buses go right by there.)
Rise & Shine Bagels has genuine New York-style bagels. Definitely open Friday and Saturday (and maybe Thursday too), 7:30am to 2:30pm. (On Bridgeport in Waterloo, see map.)
As far as I know, these are the
Edit: Also, City Cafe Bakery.