For example, what would the difference between 膝{ひざ}がガクガクする or 膝{ひざ}がガクガクしている be?

I believe the correct definition in Daijirin is 恐怖{きょうふ}・疲労{ひろう}・緊張{きんちょう}などのために体{からだ}の一部{いちぶ}が小刻{こきざ}みに震{ふる}えるさま, but that doesn't help me see how the two differ.

or the difference between:  

自分{じぶん}で出{だ}しておいてナンだけど、すごいドキドキする 怖{こわ}いかも

自分で出しておいてナンだけど、すごいドキドキしている 怖{こわ}いかも


Generally, 〜してる indicates the state of that onomatopoeia, while 〜する is describing the stimulus that caused it.

Say you are watching an intense movie with a friend.

ドキドキしてる = (My/your/his/their/our) heart is pounding

ドキドキする = (This movie is) heart-pounding

Here is an example where the two can mean different things:

膝がガクガクしてるね = Your knees are shaking (but mine are not)

膝がガクガクするね = This is knee-shaking (for the both of us)

And the most critical distinction:

あの人、ドキドキしてる = That person is excited

あの人、ドキドキする = That person is exciting

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