I ended up making most of my money by selling spare monster parts - the fangs and such that you're meant to attach to arrows, not swords. I had hundreds of them, never used them, and they aren't significantly used in armor upgrades - selling most of what I had netted probably close to 10k rupees.

Cook prime meat or gourmet meat. Skewers made out of 5 of them will sell for 135 or 315 rupees, respectively, iirc.

You can farm them quite efficiently by shooting wolves, bears, and moose in Tabantha snowfield.

There are a few good ways to do it and the comments basically cover all the best ones.

Remember that wizrobes drop weapons with gems attached that can be broken apart in Tarrey Town, so if you have a couple weapon slots to spare you can make a few hundred there.

Poe's can be converted at a rate of 150 to 600 rupees if you buy armor from the bargainer statues and sell it.

The game also gives you way more brightbloom seeds than you will ever need, so you can sell excess of those too for 2 rupees a piece. I kept a floating inventory of ~200 and probably sold over 3000 over the course of the game

Not the most efficient but buying duplicate armor from bargainer statues and selling them is a quick way to make a good amount of rupees.

that's the best way I know how (without dupes)

mine ore and sell them to the Gerudo lady near Death Mountain, she gives a premium for a rotating set of ores each time

fight moldugas -> sell the ridiculous amount of parts it drops