which of the following sentences is NOT punctuated correctly

a)I wonder why she says that. Fine as is.

b)"Give me a break",said John Insert space followin' comma and end sentence with a period, then it would be fine fine.
b) "Give me a break", said John.

c)Do you think this is funny. This is a question, it should end with a question mark, not a period.
c) Do you think this is funny?

d)When he calls,she comes. Insert space followin comma (or omit comma altogether), then it would be fine.
d) When he calls, she comes. or
d) When he calls she comes.

Also, your "a) b) c)" etc. should be separated from the body of the example sentence by a space.

Commas precede quotation marks. Sentence b) should read:

"Give me a break," said John.

Good catch, Valpower - I wasn't even payin' attention to that.

Also, may I point out that the meaning of this one is questionable...it means that she frequently says something, and you wonder why she continuously says it.

I'm not sure if that's what you meant, I think it's more likely that you wanted 'said' in the past tense.