Synonymous with the phrases "how are you" or "how are you going". Most likely derived from literal translations of similarly structured forms in European languages, such as the German "wie geht's", the Dutch "hoe gaat het" and the French "comment ça va".
"How goes it" is non-standard and is generally used as a somewhat quirky informal alternative to the more conventional questions. In this sense, the phrase may have a somewhat humorous effect.
(1) Interlocutors may respond in the same way as they would to the more conventional "how are you".
A: "How goes it?"
B: "I'm well."
(2) Alternatively, interlocutors may acknowledge the facetious nature of the structure "how goes it", and respond in kind.