I am looking for a data set that lists different kind of foods and diseases, and for each pair food-disease indicates whether the food is bad/neutral/good for the disease.
World Cancer Research Fund publishes regular reports on nutritional risk factors and diet. Documents can be found here: http://www.wcrf.org/sites/default/files/Matrix-for-all-cancers-A3.pdf http://www.wcrf.org/sites/default/files/CUP-Strong-Evidence-Matrix.pdf
Unfortunately, it's only for cancers and not available as a real dataset.
This matrix could be transformed in a dataset, but it would be quite tedious to do. These kind of datasets would be hard to create, as research in nutritional epidemiology rarely produces binary results (bad/good), and there is not always a consensus.