Question sentences with "呢/啊/呵": sounds soft, and could be a kind of suggestion or advice; somewaht like "why not ..." in English;
Qustions without "呢/么/吧/...": sometimes have a strong voice, like a command ordered by your parents/leaders.
Differences among "呢、吧、呵" depend on the different habits when speaking Chinese. People in different areas of China usually have their favourate "呢、吧、呵".