Well since Runecrafting is one of the best ways to make consistent money in Runescape and since I am trying to write guides to help people gain 99 in runescape skills that make a lot of money, I figured this guide would be one of the best to write.
I will focus on a guide for people who are higher leveled, and not for skillers. I will include Gaarhk and Abyss rcing, but any skillers or pures who are wanting to level runecrafting should just walk to the alters rather than using the Abyss or Gaarhk. So here is the best way to get 99 runecrafting including both the best for money, and the best for speed!

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Starting Off
Well I'd say the best thing to do before you start runecrafting is to collect all pouches up to the giant pouch since you will never have to go back to killing those monsters. The best method to kill the abyssal creatures is to use either ice burst or red chinchompa's. This is a multi-combat area, so you should use attacks that target multiple targets in order to kill these monsters as quickly as possible. Once you have all 4 pouches, you should either make your way over to Falador to craft air runes, or stick around the abyss to use the Zammy mage to runecraft.
In order to gain access to the Abyss, you must have completed the Rune Mysteries Quest and then go north of Edgeville into the wild to find the Zamorak Mage. I will not go into detail on how to complete this since it's a mini-quest on it's own, but simply search the Abyss on the Runescape homepage and you will find the mini-quest that you must do.

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Items Needed
-Small, Medium, Large, Giant Pouches
-All Tiara's/Talisman's
-Rune Essence (Starting elemental runes)
-Pure Essence (Catalyic runes)
-10+ Amulet of Glory (For Abyss)
-Gaarhk Pouches
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Abyss Guide
Well throughout this guide I will be mentioning the Abyss often, so I might as well put a separate section up here so everyone can get a more clear understanding of how it works and can use it throughout the entire guide.
In order to begin using the Abyss, you must first do Rune Mysteries and then do the Abyss mini-quest started by talking to the Zammy mage north of Edgeville.
Once you are done this mini-quest, you will be able to start using the Abyss. Since there are monsters that attack you and you are unable to pray inside the Abyss since your prayer is drained, it is quite difficult for smaller leveled players to use this method. The best way to do this is to wear your spottier cape, penence gloves, and boots of lightness along with perhaps black dragonhide since it is light and provides a defence bonus and along with a Mithril Pickaxe, or hatchet and an Amulet of Glory which is charged and a Ring of dueling. The reason you use mithril is because it is the lightest weaponry in the game, and therefore it is better than using rune. The reason you need the Amulet of Glory is because once you are inside the abyss and have crafted your runes, you will need to get back to edgeville to bank and repeat, so the Glory helps you do this. You need many Glory's though so that you are able to runecraft for a long time without having to charge your glory's, so I usually get around 28 Amulets which works very well. The reason you need the ring of dueling is just in case you forget to take out a Charged amulet of glory wihch happens often. Then you can still teleport to Castle Wars and bank and get a new glory out to get back to edgeville. Once you enter the Abyss, you will be skulled, drained of prayer, and attacked by many Abyssal Creatures. You must run around the outside until you find an obstacle that you are able to get past. You can use the Agility hole, Thieving eyes, and either the rock or tendrils depending on if you have a pick or hatchet to get past the obstacle inside the alter area. Once in the alter area, run around until you find your desired alter and enter the portal. Then you will be automatically inside the alter and you will not need a Talisman or Tiara. If your pouches degrade, the Dark Wizard inside the center of all these alters can repair your pouches for free.
I think this summ's up the basics of Abyss, and it should be enough to get you an idea on how it works.

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Level 1-14: Air Rune
Well from level 1-14 the best thing to do would be to craft Air runes. You should bring along your small pouch since it can hold a little bit of extra essence for you. You should be using Rune Essence here since this is an elemental rune and you shouldn't waste more money buying pure essence when you can use the cheaper rune essence. There are two options to craft Air runes. The first method is to go to Falador and simply bank at the West bank and run between the Air alter and the bank. This is the slower method since you must run both ways, but it is safe for people at any level. The second method would be to use the Abyss to craft the air runes. If you are doing this, you should have many charged glory's so that you can simply run through the abyss, craft the runes, and then teleport back to edgeville. This is the best method for people with higher defence who can stand to have higher level creatures attacking them. Make sure that you always wear your Spottier cape and Boots of Lightness if possible. You must bring along an air talisman or tiara if you are using the first method through the alter, but must not bring either of these if you are using the Abyss method of crafting runes. If you are using the abyss, you may want to begin crafting Mind, water and earth runes before fire since they are really the same distance while using the Abyss but give slightly higher experience. Simply run back and forth crafting the runes until you reach level 14 runecrafting.
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Level 14-44: Fire runes
Alright now that you are level 14 runecrafting, you should begin crafting fire runes. Again, there are two options to crafting fire runes. The best method to crafting this type of rune would be through the abyss once again. You can follow the abyss section as to how to do this if you don't know by now. If you are using the Abyss method, you should be crafting all runes between fire runes and nature runes since the Abyss makes all of the alters equally as close and you will get more experience for the higher runes. The reason you don't do these if you aren't using the abyss is because the alter is so much further away or more inconvenient that the small experience gain is not worth it. The other method which is almost equally as good requires a lot of Rings of Dueling. What you have to do is teleport to Duel Arena and run north to the Fire rune alter which is located quite close to the Duel Arena. You must run outside of the gate and go north however and not stay inside the gate. You need the Fire Tiara or Talisman for this method, and after you have created the runes, use your ring of dueling once again to teleport to Castle Wars since it is incredibly close to a bank. Then simply bank and repeat these steps until you get to level 44.
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Level 44-80
Gaarhk Rcing
Well you have finally made it to level 44 runecrafting which means you can finally craft Nature runes! These Nature runes have two different methods depending on your Summoning level.
If you are level 57 summoning, you should use the Gaarhk method to runecrafting. What you will need for this is Summoning Potions, Super Energy Potions, and Gaarhk Pouches. You will have to Summon your Gaarhk, and use it's teleport to teleport quite close to the Nature Alter. You will need a Nature talisman or tiara for this method. Once you use the Gaarhk teleport you will run East to the Nature alter and enter and craft your runes. Once this is done you should use a Ring of Dueling to teleport to Castle Wars since it so close to bank. There you will drink your super energy potion and summoning potion if needed, and renew your Gaarhk if you need. Once you are done all these things that you need to do, use the Gaarhk's teleport once again and repeat. This is the fastest way to craft Nature runes, so it is definitely recommended if you have 57 summoning. You should be using all your pouches up to level 75 when you should use the medium, large, and giant pouch and deposit your small pouch. The extra 2 essence that this pouch gives you is not worth the time you spend on the banking, so it has been proven faster to not use the small pouch once you are able to use the Giant pouch.
Abyss Rcing
Well the other option if you do not have 57 Summoning is to continue using the Abyss to craft the Nature runes. This is not as fast as Gaarhk, but it is the best alternative if you don't have 57 Summ. You should simply run through the abyss and craft the nature runes which is explained in the Abyss section above. Just keep running through, and again use the pouches which you have the ability to use to try and speed the process.

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Level 80-91: ZMI Rcing
Well in order to use the ZMI, you must have completed the quest Lunar Diplomacy in order to use the Teleport to Ouraniawhich is where the ZMI is located. Once you teleport there, you must run up towards the alter in the center of the lava area and pray if your prayer is low and then climb down the ladder. Once you are here you must run straight through all of the Zamorak followers where you should pray range and wear Black D'hide in order to stop the mages from properly hitting. Just run through with your prayer on and once you get to the alter craft your runes normally. Once you are done that you can either teleport to Moonclan since you will have created so many new runes, or you can teleport to Castle Wars or anywhere else. As for banking, you will have many different types of runes, so they best way to bank would be to have a special tab open for your runes where you could use the Deposit All button to bank everything and then quickly withdraw your pouches. This is much faster than depositing all types of runes individually. And once this is done, you must once again teleport to Ourania and repeat the steps. You craft many different types of runes at a random rate, but you receive 2x the experience for crafting these runes as you do normal runes. The higher your runecrafting level, the higher the runes you receive so it is best to only start at 80 since you are able to still profit and gain extremely fast experience. This is as best as I can explain ZMI since it is quite simple, but if you have any further questions you can comment and I can try to help.
If you haven't done Lunar Diplomacy you should continue to do Natures all the way to 99, but it is strongly suggested that you do Lunar Diplomacy since the experience is extremely fast and can get you to 99 Runecrafting very quickly.

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Level 91-99
Well there are two options once you get to level 91 runecrafting. You may either stick with ZMI rcing which you have been doing since level 80 runecrafting since you will be able to make smaller profits and still get to 99 much faster, or you can go back to Rcing nature runes where you will receive Double natures which means an incredible amount of cash/hour. I personally suggest runecrafting nature runes since you will receive upwards of 900k/hr in Runescape money, and therefore in a day you can get a few million GP. But it really depends on if you are runecrafting for the Cape or if you are runecrafting for the Money.
Both the ZMI and the Nature rune crafting methods are explained above, so there is no need to re-state what I have already said. Just choose whichever method you want, and have fun!

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Conclusion:
Well Runecrafting is a very tedious and annoying skill to train since it takes so long and can be so boring. I strongly suggest taking breaks in between levels to do other stuff to keep you sane! I hope that you guys are all able to gain more knowledge from this guide, and if there is anything you feel I have skipped over, please let me know.
Now that you are done runecrafting, you should be incredibly rich since it is the best money making skill in the game. With your new money, you will easily be able to get other 99 skills that you must pay for such as Herblore, Construction, Fletching (Addy Arrow Method), Cooking, Smithing, Summoning, Prayer, or any other skill you must pay for.
Thank you all for reading, and since it is a large guide written all by hand, there may be things i missed, skipped, or said incorrectly, so please let me know if this is the case!
-RS Junkie

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Other Runescape Guides
99 Hunter Guide
99 Fishing Guide
99 Fletching Guide
99 Mining Guide