List of Chinese characters not used in Mandarin/putonghua
The only online dictionary database I can find is 《新华字典》. It is a Microsoft Access database containing 20823 characters. You can run a query on the database and search for "方言" in the "xiangjie"(详解) column. There are shortcomings however, 20823 characters may not be comprehensive enough, and it usually doesn't tell you which dialect the character is used in.

You can download the dictionary database file here.

For Cantonese, there is a convenient list circulating around called 粤语字打法大全. Wikibooks also has a character list but there is no definition of meanings. You can find more if you search 粤语字 online.