If it were just you going, how would the sentence go? I will meet you today or Me will meet you today? It doesn't change if Bob decides to come as well.
No it does not change. The way I was taught was if you removed the other people in the sentence for a list, does it make sense. In this case, Me will meet you does not make sense, however the sentence "you will meet Bob and me at the store" is correct in this case. "You will meet me" makes sense while "you will meet I" does not.
"Bob and I will meet you today" is grammatically correct since "I" is a subject pronoun—not an object pronoun. "me" is an object pronoun, and should NEVER—yes, I mean it—EVER should be used in the subject of the sentence.
Your answer, though a good one that I agree with, reminds me of the joke my 5th grade teacher put on the board forty years ago. " 'Me' can never be the subject of the sentence," just proves the exception to the rule. In that sentence, which word is the subject...?