Chime in here guys, I don't really have any citations to hand, but I definitely have the impression that Varys fed Aerys' paranoia and probably intentionally (though, strangely, he did, allegedly, beg the king not to open his gates for Tywin). Am I totally making that up?
I don't have quotes, but the line you are referring to goes something along the lines of: <Aerys was seeing traitors in every shadow, and Varys was pointing out the ones he missed.> But I don't think he was making him more paranoid than he already was, attempting to further his downfall.
Varys was, in the 2nd or 3rd book, described as the only one pleading with the king to NOT open the gates for Tywin Lannister during Robert's Rebellion because he knew his true purpose. He didn't want the city taken, and the Targaryens cast from power. I believe he truly was a Targaryen loyalist and was pointing out the real traitors.
Yes Aerys was the mad king, but according to Ser Barristan in ADWD he didn't start out that way. I think it was after his rescue from Duskendale and his time in the dungeons there that he started to go truly mad. And those he burned were high lords, not the scores of innocent townfolk that suffer during civil war. Varys is on record saying that the innocent are the ones who suffer when the high lords play the game of thrones. He doesn't want a game of thrones and could care less about the players. He wants the king on the throne who can command obedience from the realm and keep it from bleeding. He knows what it's like to be weak and alone, that's how he grew up. He doesn't want others to suffer as he did.
He knew that the Lannisters were aspiring for the throne, he knew this was lead to civil war, so he cultivated as many Targ options as possible to groom them to end the coming war and bring the realm together again.
<From the very last chapter in the book......SPOILERS if you haven't read it!>
We have little to go on to peg his true motives it's true. Everything he says is a lie, always playing the mummer. But in the very last chapter you see his contempt for the high lords and praises Aegon's return. He preaches how Aegon was brought up among the common folk, the ones he should be protecting, not using for his own games. There is no reason for him to lie to a dead man, it would not serve him.
"Whom do you truly serve Lord Varys?" - Eddard Stark
"The realm my lord. Someone must." - Lord Varys