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
