You get ~1k for completely exploring a Divinity Reach or Lion's Arch I think. I'm not sure if it scales to level. If you completely explore all of Queensdale you get about 1k exp, green items, transmute stones, and like 30-60 silver.
I'm pretty sure they came from zone completion too. I only opened one mystic chest from all the betas and I have a bunch of transmute stones that I know I didn't buy or get from the chests.
Don't think it's the mystic boxes. When you complete a zone you get some green pieces, some XP, gold, karma and a box. I always got transmutation stones from them though.
