Why wasn't Arlong in Impel Down during the Impel Down Saga? He was a known member of Fisher Tiger's crew and became a merciless dictator in East Blue. He had the highest bounty in East Blue at the time, and when Borsalino captured him, he was sent to Impel Down. So why was he not there during the big jail break? 

I doubt he got left behind, because Buggy did most of the freeing of prisoners.
We currently have the following timeline of things happening to Arlong:


Arlong gets beaten by Borsalino (Kizaru) and sent to Impel Down.
Arlong is released from Impel Down when Jinbe became a Shichibukai.
Arlong had a fight with Jinbe and started the Arlong Pirates and went to East Blue and settled on Cocoyasi Island.
Luffy and crew follow Nami to Cocoyasi Island where Luffy beats up Arlong.
All of Arlong's crew get arrested (exception: Hatchan) by marines.


I skipped a large chunk between points 3 and 4 because it's irrelevant. You can find all of Arlong's history here.

At point 5 when they got arrested you would assume that he would have been sent to Impel Down again, but it is futher unknown what has happened to Arlong as it hasn't been shown or told in the anime or manga.