What is the best way to get rupees?

I played through the entire game, collecting gem stones (Ruby, Diamond, Sapphire etc.) as I went, and never found any particularly useful purpose for them beyond the very occasional item crafting and upgrading purposes. I kept expecting them to be useful someday, but they really weren't. Certainly no need for a huge pile of them anyway.

Sell off all but 10 (just in case) of every gem type you have and never look back.

I'm finding that pretty much everything has some use somewhere down the line. Plants and fruits seem to be the most abundant and least useful but you don't get an awful lot for them.

However the advice you are (frequently) given in game has worked the best for me; sell gemstones. Luminous Stone sells for 70 Rupees and is very easy to find. Just grab a hammer and climb a mountain at night. Midway through the game (having not sold any) I found myself with about 50. They do have various in game uses but they are reasonably easy to come by so I wouldn't worry too much.

Rubies, Sapphires and Topaz are even better. They sell for a lot (180 - 240 if I remember right) so you don't need a lot to make money. You can tell which ore deposits have gems in (they are shiny and gold) so mark them on your map and come back frequently to see if they've respawned. Or hunt Talus, once you get the knack of killing them (and particularly if you have access to the Goron special weapon) they are pretty easy and give you loads of gems and ores. The gems do also have various uses in the game, but I've found they're more useful to sell then any other potential use so far. Amber and Opal are needed for various armour upgrades but you can find quite a lot of them so they are good for selling too.

Monster parts are tempting, as some can fetch quite a lot, but you need them in abundance for upgrading armour so I only tend to sell things i have loads of (100+) and even then I save them for Kilton...

So far I've not really had to wait long for anything money related and haven't found anything where I've thought "Damn, wish I hadn't sold that!" by mostly just selling gems.

Farming Farosh Horn Shards! Go to the cave just north of Riola spring equipped with

1. lots of arrows and a decent bow
2. wood
3. some sort of flame weapon

You want to be inside the cave when you set up your campfire so that when it rains it doesn't put your fire out. Set up your campfire, then sit and wait until morning. Farosh will spawn right after you wake up, at which point you use the paraglider to lift yourself up a bit (he'll create an updraft) and then fire an arrow at his horn! You don't need to go grab the shard right away either because it won't disappear as you pass time. So then you basically use your flame weapon to re-light your campfire. Rinse/repeat until you feel like collecting your shards, which will sell for 300 rupees each. Even if you miss the horn, his scales sell for 150. I've been doing this since I found out about it and now I have 47,000 rupees :)

This is a debated method. Some say cooking is the best, but I think that the effort it takes to find ingredients combined with the cost of losing weapons and the time it takes makes cooking a slower method of obtaining rupees. From googling things, you will find that there are 2 major suggestions

1. Spam mini games and exploit the winnings
2. Sell food

For me the snowball bowling mini game was the best way to get rupees in Breath of the Wild. Once you get the hang of it, you can easily afford the ancient armor set in a few hours. Keep throwing the snowball the correct way over and over and it is an easy 200 rupees every single time. No wear and tear on your gear, no enemies and no travelling. You also don't need to worry about your inventory filling up etc.

Each blood moon kill all the Lynels, Hinoii, Talus and Moldugas. Then farm Mt. Satori specifically for Endura Carrots but get everything you can. For Talus focus on the fire ones in Death Mountain, they're really easy to beat and drop higher level gems.

• 4 Lynel Guts + 1 Insect made into Elixir will net you something like 2400g
• 4 Molduga Guts + 1 Insect made into Elixir will net around 1400g if I remember right
• 4 Hinox Guts + 1 Insect made into Elixir will net around 900g
• 5 Endura Carrots dropped made into a meal will net 440g

At early levels I'd focus on Mount Satori for your financial needs.