I'm gonna list some ways to make money. You probably know most them, but yeah.
Extremely obvious, but let's face it, most of our money comes from defeating them.
Gym battles give you more money than Trainer Battles, and Re-Matches get you even more.
Selling items such as:
Items that you don't need can be sold at the Pokémart, however, they do not accept Key Items.
Use Theif on Clamperl when diving. There is a 5% chance for it to have a Pearl, and these sell for quite a large price.
The Elite Four get you the most money out of all the 'Trainers'. Pair this up with an Amulet Coin and you'll be swimming in cash! Well.. Not exactly swimming but you get what I mean. :P
The Amulet Coin doubles the amount of money that gets rewarded for battles if the Pokemon holding it is in battle. If you use this frequently with Trainers, Gyms, E4, etc. then you should get a fair amount of cash.