A bunch of quests throw rupees at you, and monster parts and gem stones sell for a bunch.
Basically you need to figure what you need to hoard and what you have in excess. You get 12 dragon shards on a 10 minute respawn timer that are there every time you go for an item, they sell well too.
I've yet to have an economy issue, and I'm wearing a 3/4 set of Fierce Deity armour I got from a quest chain.