Speaking as a DM currently running a combat including not only 8 PC-controlled characters/companions but now with several PC-summoned Lantern Archons versus a large number of opponents in their overlapping auras of menace, I have to say: this is Shoddy Design(TM). 
What a book-keeping headache. 
The mechanics here are in serious need of an overhaul, or at the very least clarification.
Auras ought to >absolutely specify< in the core rules that their effects only remain while you're IN the aura. 
This ought to be obvious but it's contra-indicated by other wording in the aura descriptions.
Persistent effects once you've left the aura? No thank you. 
24 hours duration? Why? Confusing, extremely unbalanced and illogical (unless you're in the presence of the aura's source continuously).
The confusion over stacking could be easily cleared up. 
The tedious book-keeping could be eliminated.
E.g. Lantern Archon's Aura of Menace:
"Aura of Menace (Su) ... or until they successfully hit the archon that generated the aura." (Source 1 of the book-keeping - I have to track who hit who and adjust only that one foe's penalties each time a foe lands an attack - great!)
How about 'or until the archon that generated the aura >is damaged<' instead?
1 hp damage, whether from you or your buddy, or anything else for that matter - hey, that archon's not so menacing now - that aura is dispelled for ALL. 
'...is hit' works equally well for me. 
'hit by...' makes comedy steam come out of my ears.
"A creature that has resisted or broken the effect cannot be affected again by the >same archon's aura< for 24 hours." (Source 2 of the book-keeping: even if the penalties don't stack I have to track each creature's aura effects - on everything that wanders within range - separately, cos if it leaves the aura and comes back, well, I need to know not to roll another save.
Try 'A creature that has resisted or broken the effect cannot be affected again by an aura of menace from the same type of archon for 24 hours.' 
Yes, this weakens auras' effectiveness. I personally don't mind that. My fun is actively reduced by needless, fiddly book-keeping. My proposals are a bit 'shoot-from-the-hip' - I'm sure they could be improved. A little streamlining and consistency could go a long way.
Also, aura of 'menace'? Screams mind-affecting fear effect. 
Look at Frightful Presence for a parallel. 
I don't find the 'vermin/constructs/undead are rendered ineffective by waves of sheer awesomeness' exaplanation very compelling. YMMV.