I've done 3 trips on Georgian Bay in the past few years.
First trip was the Mink and McCoy island group on the eastern side. Enjoyed it for being my first trip to GB, but not as much as I've enjoyed the Bruce Peninsula and Killarney area.
In 09 we paddled from Lions Head on the Bruce Peninsula to Tobermory and then out to Fathom Five marine park. There are a limited number of campsites available to kayakers, but it was adequate. There is a site called Reeds Dump on provincial land north of Lions Head, then a longish 23 mile paddle to High Dump in the BP National Park. Further on we camped at Storm Haven in the park before heading to Tobermory. Both of the sites in the national park have platforms and can be reserved in advance. The last night we camped out on Flowerpot Island, the only place you can camp in the marine park. That site has to be acquired the day of at the visitors center, which requires you to walk about a half mile from town. The entire shoreline of this trip was just beautiful with high rock cliffs, caves and rock beaches (don't expect any soft landings). Hiking the Bruce trail while there is well worth your time!
This past summer we continued our journey. 3 of us put in at Tobermory and crossed to Manitoulin Island, camping on Yeo and Rabbit Islands along the way. There was some disagreement about who's islands those were. Ontario parks says they are crown land and we could camp on them without permits (south of French River) but the first nation people claim them as theirs. Either way, we had no trouble at all and some first nation fishermen even brought us some fish the morning we were on Rabbit Island.
We chose not to camp on the east coast of Manitoulin because it is first nation land. They say you are welcome to camp there, but they have to know when and where and ask for $50 per person per night for backcountry camping. We decided to rent a cabin on Elm island off the northeast tip of Manitoulin from a local man. After a 3 night stay there we met up with 4 more paddlers (total of 7) and headed east along Badgely Island to Killarney.
The geology changes often between the Bruce Peninsula and Killarney and I never tired of the variety of rock formations. By the time you arrive in Killarney it has become pink granite, just beautiful. We continued to paddle on to the outer islands of Phillip Edward Island for another week of camping, including trips out to Hawk and Green Islands before heading back to Killarney, along Badgely Pt. and back to our take out on Manitoulin. We had managed to get some of the second group to bring our vehicle over on the ferry with them and we all ferried back to Tobermory, but I'd be tempted to paddle back the next time. The whole trip was gorgeous, we had pretty benign conditions, which doesn't often happen on GB and I'd repeat that 2 week trip in a second. Pics of both trips can be seen here.http://picasaweb.google.com/shafra9
The first is Bruce Peninsula, Air, Land Water and the second longer trip is Tobermory to Killarney and Beyond.
Sorry to ramble on so long! Hope this helps and please don't hesitate to drop me a line if you have questions.