My brother used his at the Nickelodeon Hotel, but I don't know whether you can still do that or not.
As far as hotels with shuttles, except for those in the immediate vicinity of the airport, I've never come across any. There are shuttles that you can pay for that will take you to the hotels though (such as Mears).
ETA: There's a Staybridge Suites on International Drive that has transportation to the Disney parks and is also on the I-Ride Trolley line up and down International Drive (only about $7 for a week's pass). That would get you around pretty well, but you'd still have to take a shuttle to get there. I've stayed in the 2BR suite there, and it had a full kitchen plus daily breakfast included.
