How can I get more of each evolution stone?
You can get some from the Secret Super Training levels.
From Serebii's Guide to Super Training:
If you are using a Pokémon who has got maximum Effort Values, you will gain access to Secret Super Training. [snip] ...these games give you more than just bags for core training, they also have a chance of giving you rare items. These items range from items such as Clever Wing, to evolution stones. [snip] You can also get various healing items, items such as Stardust and hold items such as Hard Stone.
Apparently they are rare and depend on how well you compete.
Rom016 has been doing some of these, and it appears that the drops are not based on how well you compete. They do still appear to be rare, however.
- The Troubles Keep On Coming - Wing Items
- The Leaf Stone Cup Begins! - Leaf Stone
- The Fire Stone Cup Begins! - Fire Stone
- The Water Stone Cup Begins! - Water Stone
- Follow Those Fleeing Goals! - Thunder Stone
- Watch Out! That's One Tricky Second Half - Dusk Stone
- An Opening of Lightning-Quick Attacks! - Shiny Stone
- These Long Shots Are No Long Shot - Dawn Stone
- Scatterbug Lugs Back - Wings
- A Barrage of Bitbots - Wings
- Drag Down Hydreigon - *Moon Stone, Sun Stone**
- The Battle for the Best: Version X/Y - All of the above
Besides super secret training you can also farm some of the evolution items. Dragon Scales are a hold item for Dratini, sun stones can be held by Solrock, moon stones by Lunatone, Stelix holds metal coat ETC. According to serebii.net(I had to look it up) king's rocks are held by wild Poliwhirl, Poliwrath, Politoed, Hariyama and Hawlucha.
To speed your search for these wild hold items it's usually best to get a pokemon with the Frisk ability and teach it either "Thief" or "Covet".
Another thing you can do that's a hold over from gen 3 is to get a few pokemon that know Pickup and get random items that way. You can usually get a few evolution stones and other items depending on the Pokemon's level and where you are in the game.
There are 2 more ways to get additional Evolution Items and both are somewhat more efficient than Secret Super Training (unless you're very skilled at them and handle them in little time). I'm only mentioning ways to get an infinite amount of them (given infinite time), note that you can get any amount of each Evolution Stone in-game with the second method and any amount of each Evolution-related Item on the Internet as long as Pokemon doesn't take down this option (which is always possible, see Dream World).
The first way is 3ds.pokemon-gl.com. In the PokeMileage Club on Global Link, you can spend 100 PokeMiles to Play "Ballon Popping". There are 3 Levels and each yields different Items, which are drawn from a pool consisting of all EV-resetting Berries and all Evolution Items (Stones as well as stuff like King's Rock). Before starting a game, you can view the Items available in each Level, so you can pick the Level with the Item you want. Then it's just a matter of luck, what Items you receive seems to be random. See my question about the mini-game for (not that much) more detail.
The other and in my opinion best way to "grind" Evolution Stones (but only those, other Evolution Items are not available this way) is Route 18's Psychic Inver. Once a day, you can get 3 copies of one Evolution Stone from him if you beat him in an Inverse Battle without any of your own Pokemon fainting, provided you hit the right number of super-effective and non-effective attacks. This is a rather complex process, but I collected most information about it in my answer to a related question (including a very reliable strategy to get those Stones).
You can get all the evolutionary stones from so-called "Secret Super Trainings", unlocked when you complete all the Super Trainings with a single Pokemon. Completing these Secret Super Trainings has a chance to give you evolutionary stones, from Water to Dusk to Dawn Stones.