This is very difficult to pull off, but I have tested it, and it does work. I was somewhat skeptical when Mence Master reported this discovery. I asked lots of questions to ensure that the theory was consistent. Now there is solid evidence as well.
Much of this information is paraphrased from parts of Smogon with my comments added.
Recently, I was able to validate that Pokemon Emerald can produce IV and nature clones. On my recent emerald file, I caught a Shining Poochyena and a Voltorb. They both had Lax natures. It didn't occur to me at that time that they had the same IVs and nature.
Emloop has 3 main programs:
1) A timer used for timing the soft reset. If you put in the frame you want in the upper left corner, it calculates the time you need to wait to start the battle. The two boxes on the right that are on top and bottom of each other allow you to adjust the timer. The top box allows you to set a timer before you soft reset, so that you can time the soft reset correctly. After that, the main timer starts. The second box allows you to short the timer by a number of seconds so the timer hits 0 when you need to use Sweet Scent or start a fight with a legendary.
2) A program that allows you to access a list of pre-determined IV's and natures. You will see several check boxes with numbers next to them. If you want to search for a specific frame with a specific IV, put a number in that box and check it when you search. Only check one or two boxes at a time, as it is very unlikely you will be able to find more precise stats within a certain amount of game time.
I would enter 50000 as the number of frames. You can do more if you want, but it will require longer waits for frames that come later.
The spot below the number of frames is the nature. This is a translation guide for the various natures:
http://egg-in-oven.hp.infoseek.co.jp/pokemon/poke-en/nature.html
I am not sure what the box below that is for, but the two boxes below are where you put in your ID and Secret ID (SID will be discussed later). You will need both to look for Shining Pokemon. To look for Shining Pokemon, check the box next to the text with the 5-point star (not the asterisk).
One of the buttons allows you to run the search. Clear out the box above the text output after you search, otherwise, it will not run the same search again (it will search for later frames).
3) A Secret ID calculator. Normally, only an AR can be used to find your Secret ID, but if you have a Shining Pokemon you caught in Emerald, and the same file is still active, you can use it to find up to 8 different SID's. These IDs are used for extra operations in the game, such as ensuring that two Pokemon with the same original trainer ID and name but different game packs aren't considered the same. The SID is also used for determining Shining Pokemon personality values and Mirage Island numbers. So far, my experience has been that each of the 8 possible SID's produce the same pattern of shiny frames. Is this true for everyone else who has tried this?
I went ahead and plugged the Shining Voltorb's IVs and nature into this program on Smogon to calculate the personality value.
http://www.smogon.com/forums/showthread.php?t=50696
Then, I went ahead and plugged the PID into Emloop and found 8 possible SIDs for my game. All 8 of those SIDs produced the same "shiny frames" (originally called shiny numbers in the other thread). Now, I know exact moments in my Emerald game when Shining Pokemon appear.
I now have a shining Tentacool, Magikarp, Loudred, Feebas, and Hariyama in only a 3 day bandwidth. As expected, many of them have the same nature and IV's.
While this process sounds easy, it is actually very difficult for the following reasons:
1) There are 60 frames that are generated in 1 second. Timing the frame correctly is very difficult.
2) Emloop's timer doesn't exactly match the time that passes in Emerald, requiring adjustments.
3) Wild Pokemon in the grass require Sweet Scent for good timing, requiring more adjustments.
4) Emloop is in Japanese, so it requires some experimentation to figure out how it works. There are some guides on Smogon (in the URL WPM posted) that can help with that.
Having a Synchronizer in the lead spot in your party has been reported to cause the RNG to skip to the next frame with the nature that is the same as the Synchronizer. However, lately, the RNG has been doing something weird where if I am not using a Synchronizer, I consistently get frames that are as much as 30 frames apart from each other, but if I do use a Synchronizer, the RNG jumps around a lot in random directions, even skipping over multiple natures of the same nature. For instance, I might be timing for frame 10000, but it jumps to 10100, even if there is the same nature at 10024, 10050, and 10072, etc. On some occasions, I get IV's that aren't even on any of the 3 lists there (wild Pokemon is method 2)!
So yeah, this requires a lot of trial and error. Good luck if you decide to try it! There still appear to be new discoveries made around this, so stay tuned!