Jangojess is correct in their analysis of this problem - Japan is not a culture; Japan HAS a culture. Because of this modifier issue, we can rule out A, B, and C. D and E, on the other hand, use "Japan's is a culture of ...", where the possessive Japan's implies "Japan's [culture] is a culture of ...". This makes more sense.

This leaves us with D and E. If we see that "which" does not have a comma before it in E, we can eliminate it right off the bat - "which" will always come after a comma. However, there is an additional problem with E. We notice that E includes the word "of" twice.

So while D can be interpreted as:
Japan's [culture] is a culture of accommodation and constraint. [Japan's culture is] a system of forms, etiquette, and images that makes the ever-present congestion tolerable.
E on the other hand can be interpreted as:
Japan's is a culture of accommodation and constraint. [Japan's culture is a culture] of a system of forms, etiquette, and images which makes the ever-present congestion tolerable.

This makes E somewhat redundant and different in meaning than the original sentence. So we can rule out E and select D.