I thought Arlong had died at Arlong Park, but then in the Duval arc Hachi said he was in prison. My inmediate thought after Luffy started meeting old characters in Impel Down was that he would meet indeed Arlong somewhere there, then I thought he was free and waited to see him in the Fishman Island arc. I now doubt it though, if he was there he would've appeared by now, specially after Madam Shirley... well, you know who she is xd
I once read a theory that Arlong could have been sent to Enies Lobby, but I don't find it plausible, I don't think he was that important to be sent to EL. Personally, I think he was locked in the marines HQ that aren't in the Grand Line, very probably in East Blue... you know, where Nezumi worked.
And yeah, that got me sad too

Shouldn't you put that last line in a spoiler though? It's a pretty bad spoiler for those who haven't caught up yet...