You know how in English instead of saying 'where are you going?" we say "where are you going, huh?" or "who is she, exactly?" as opposed to "who is she?" or even: "just what are you doing here?" as opposed to 'what are you doing here?" The "exactly" "huh" and "just" are not necessary in those sentences no more than the 呢 is in '你怎么去呢?"(how come you're going?) In English we can imply many different things just by changing the tone of our voice(or adding an extra word) In Chinese, you can't do this, because its a tonal language. Hence, the use of ending particles such as 吧 and.呢(to change the tone of the sentence) Here's an example: 虽然我不喜欢我哥哥，但是我去他家(even though I don't like my older brother, I'm going to his house) 你怎么去呢？(Well, how come you're going?) or another example: 英语很难学. - English is so hard to learn. 所以呢，你应该常常学习！-which is why, you should study often! Sometimes 呢 is used when asking for someone's opinion: Imagine you can't decide something, so you ask your friend: 我该穿哪件衣服呢？(which outfit should I wear?) or a situation where time is running out and you're panicking: 我应该做什么呢？"What should I do?" The last thing I want to add, the same way we use 呢 as a way to restate a question without repeating the WHOLE entire sentence, like in:　 好久不见，你好吗(long time no see, how have you been?) 我很好,你呢？(I'm good, and you?) You can use it in a situation like this: 你多大了？(how old are you?) 我看起来多大呢？(well, how old do I look?) Its appropriate and makes sense to add "ne" since the person originally asked you the question, but you didn't answer and you asked them. I hope this helps you and clears up confusion :D

加“呢” 的意思是说话都带有种反问的语气，听起来更委婉。

Thanks to all for the thoughtful inputs. It seems everyone has a different, but relevant perspective. I think Randy has the grammar part right: the the 呢 is expresses "how about you" - just like 你呢. So, it indicates interest or concern towards the person being spoken to. And I think this is why the Chinese speakers say that it gives the sentence a more friendly tone.

we usually use the words just like “呢 哦 吧”to change the tone of the sentence，then the receiver may feel it's a comfortable tone ,not a stiff one. just like why we say let's go not go.

Of course you can just say:你怎么去 To me, it's just mild and indirect with 呢,