It's not technically in Downtown Disney, it's at the Grand Californian, and is accessible from Downtown Disney, but Napa Rose is absolutely amazing. One of the best meals I have ever had, anywhere. It's a splurge, but worth every penny.
If it must be in Downtown Disney, as other posters have mentioned, all of the restaurants are good; it just depends on the type of cuisine you're looking for. Naples has very good Italian food, for example; that's a regular spot for me when I'm out there.