A spy can be sent in before the circumstances arise that even require a spy. The advantage is that the spy is viewed by insiders as a fellow insider before danger arises. This was the case with Ser Jorah. Oh no, I just realized I wrote Jorah in my previous post when I meant Jeor! Doh!
Anyway, Dany viewed Jorah as loyal to her even before Viserys died. Because Jorah was there before Drogo's fall, Dany's flight, the awakening of the Dragons, and her successes Jorah was seen as an intimate confidante of Dany. He was viewed as an insider because he was with Dany before the **** hit the fan.
Also, remember Hugh, Jon Arryn's squire? Lysa and/or Littlefinger got to him after he'd been Jon's squire for a while. She/He/They bribed Hugh into murdering Jon. Enter Ser Hugh of the Vale with brand new armor! People can be bought.
The masters of intelligence and deception in ASOIAF include Baelish, Illyrio, Varys, and Tywin... Doran might be on the short list also. I think these players are shrewd enough to have "little birds" from all corners of the Seven Kingdoms on their payrolls. Spymasters don't know when important information might come from Dorne or when action might be needed at the Wall... they need agents already in the field to get the information or to take action.
Let me give two other possible examples of possible spies. The first is an insertion of an agent into an unsuspecting man's entourage before he gains power. The second example is of bribery.
How did Shae wiggle her way into Tyrion's heart so quickly? Bronn told Tyrion he took her from some hedge knight. Shae had no qualms about Tyrion's appearance even though she was probably only approached by Bronn minutes before. Then Tywin forbade Tyrion to take her to KL.
So what if Shae was actually a spy? I know I've posted on this subject before, but bear with me. Tywin or one of his men pays Bronn to bring Shae to Tyrion. She would have been prepared for his grotesqueness, his vices, and his specific tastes by Twyin's spies. The best way for Twyin to get Tyrion to do something is to forbid him to do it... ala Cersei trying to get Robert into the melee. Then Tyrion keeps Shae (Tywin's spy) with him just to spite his father. Tywin got updates and reports from Pycelle, Cersei, and maybe Littlefinger, but according to this theory he got the best inside information from Shae.
What was Tywin's biggest problem during the War of the Five Kings? Leading the army to victory while running the government. He could not be in two places at once. Over the first three books we see how much Tywin distrusted and despised Tyrion. There is no way he'd have sent Tyrion to rule without a reliable spy or two or three to tell him what Tyrion was doing. Shae seemed to turn fairly easy and betrayed Tyrions's intimate secrets... surely "my Giant of Lannister" was not evidence of regicide... no, that was just being mean.
Why was Shae in Tywin's bed? Perhaps this is how she made Tywin's acquaintance in the first place.
I think Tywin had another spy in Tyrion's midst... Bronn. Sure, Bronn was chance met on the road. But he changed allegiances for a better paycheck quickly. I think Bronn was bought off when Tyrion returned from the Mountains of the Moon. Shae was never privy to the planning of operations, but Bronn was. Why did Bronn suggest killing Joffrey? He would not benefit from it. If Bronn was Tywin's agent, Tywin could have told Bronn to suggest it to Tyrion. Killing a wild and unstable king was "unthinkable, but obvious", if I may quote from Shogun. It seems that after Tywin returned to be Hand he might have killed Joffrey and replaced him with Tommen. Tommen would assure a time of peace for the Lannisters to consolidate their hold on the Iron Throne. Killing a king is a messy job and Tywin had done it once already. If he could manipulate Tyrion into doing it for him, then he'd have a major problem solved and a ready scapegoat if need be.
Bronn did not even testify against Tyrion... he just walked away. And for this he was made Ser Bronn of the Blackwater and potentially Lord Stokeworth? Come on... he had to have been doing more for Tywin than just walking away from Tyrion after Tyrion was hung out to dry.
In conclusion, I have two small evidences (and two larger speculations) of planting an agent before an enemy knows it needs to protect against one and of bribing someone to become a spy. I think Illyrio could have bought Qhorin, Donal, Edd, or Jeor. I also think that Illyrio could have turned Aemon into his agent years ago and that Aemon could have influenced, persuaded, or bribed Qhorin, Edd, Donal, or Jeor into doing his pro-Targaryen work.
I admit that the Aemon as Jon's guardian is pure conjecture, but it is possible. Well, it's possible until you guys poke some real holes in this theory.