What do you mean by that?
What do you mean "lunch is on me"?
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There are a lot of meanings of 'by.' What is the meaning of 'by' in the two sentences?
The word "by" is only in the first sentence. That word has MANY meanings!
http://www.merriam-webster.com/dictionary/by
Scroll down until you see definitions 6a and 6b. Those are probably the closest definitions you'll find for the usage in sentence 1.
In this dictionary, look at definition 6d:
http://www.learnersdictionary.com/definition/by