I've just updated Encode-O-Matic with a Guess Input Encoding feature. When you start Encode-O-Matic or when you use the 'Guess Input Encoding' menu item from the 'Tools' menu, Encode-O-Matic will try out various combinations of encodings and guess at which set seem to apply to your input. For instance given the following text, Encode-O-Matic will correctly guess that it is percent encoded, base64 encoded, deflate compressed text:
It should work fairly well for simple things but I did pick 'Guess' for the name of the feature to intentionally lower expectations. It doesn't currently apply to character encodings but that may be something to consider in the future.