This is what the Warcraft RPG books say about the Stormwind Stockades and Vault:
Those criminals who survive arrest and trial reside in one of the city’s two prisons. Common criminals from pickpockets to murderers stay in the Stockade. More dangerous types — demons, rogue mages and the like — are left to rot in the Vault. I don’t like coming near that one; it’s surrounded on all sides by water, and I’m assured it is safe, but the hairs on my feet prickle when I get too close to it. Keeping those demon abominations alive in there is just asking for trouble...
...The city’s two prisons, the Stockade keeps the everyday criminals, while the Vault houses those who have no right to live but we don’t have the means to kill easily — demons, ogre mages and other nightmares.
For starters, I don't think it should be an outright 20-40 man raid, nor a 5 man dungeon. Instead, take the UBRS angle with it and add Stormwind Vault in as a 10-man or 15-man mini-raid. Perhaps the reason us adventurers have to go down there and clear it out is because Onyxia caused one last event of chaos before leaving Stormwind, killing the wardens of the powerful prisoners and breaking the seals of the prisoners in the Vault. The map of Stormwind Vault shows there being 5 distinct, big rooms for possible boss fights; when it comes to rogue mages and powerful ogre mages, someone like Glubtok from the Cataclysm Deadmines springs to mind as a boss that could work well, for instance. There could be a necromancer locked away in the vault, using the chaotic situation as an opportunity to build an undead army out of the bodies of dead inmates around him, and a part of the Vault filled with many Horde prisoners; the third boss could be a team of 3-5 Horde champions. But at the bottom of the Vault lies a demonic influence; the second to last boss could be a warlock summoning demons running amuck, with a fearsome doomguard as his guardian, and the final boss could be a particularly notable demon, one with the same "demonhunter" model as the "Atiesh" demon or the infamous "Cleaner".
But the reason Stormwind Vault has always been a confusing idea to speculate about is because there isn't really a Horde equivalent. What Horde city would have an area that not only could fit well as a dungeon, but could conveniently be turned into one and is also mostly unused? Well, there is one...
The Ring of Valor has been criminally underused in Vanilla-Wrath, and while it was originally intended to serve a purpose similar to the Gurubashi Arena (a place that is now easily accessible on this server), it could perhaps instead be the Horde-equivalent for the Stormwind Vault, instead working in a manner reminiscent of Trial of the Crusader from Wrath of the Lich King. While the Alliance is in the midst of political turmoil threatening Stormwind, the Horde instead holds a love for gladiatorial combat, and calls out to any adventurers brave (and greedy) enough to prove themselves in the arena. The loot would be of similar equivalence, but the bosses could vary much more; these bosses could include exotic beasts like a Devilsaur, a mighty Elemental (maybe an Air Elemental as those are seldom seen compared to the other types in Vanilla), Alliance prisoners forced to fight in the arena, a master Venture Co. engineer with many tricks and mechanical creations up his sleeve, and an imposing Giant to round it all off (those who watched the old WoW Beta trailer might remember that fight with a titanic watcher in Gurubashi Arena near the end).
Let me know what y'all think off these ideas and what ideas you personally have, of course. :)