The prayer skill has always held a certain amount of notoriety. This combat skill, which benefits all types of combat (although melee slightly more than ranged and magic) is one of the oldest skills in the game, being introduced shortly after the game's release. The skill determines the player's ability to invoke the favour of the gods to aid them in various ways, with the actual level not only determining what help the player can ask for but also how long it can be maintained before their Prayer points need to be recharged.
When the prayer skill was originally introduced, it was split up in PrayGood and PrayEvil, although this split was canceled long before actual prayers became available. While it was listed in the skill window with other 'useless' skills such as carpentry and tailoring, it actually became possible to gain experience in the prayer skill with the introduction of the bury option for monster bones and the Restless Ghost quest. To make matters even more confusing, some of the prayers that would eventually be usable in the game were listed under the Magic skill, which was also split up into good and evil. Most of the prayers (which couldn't actually be used) were listed under the 'good' form of magic, while what was to become the starting spellbook for all players was listed under the 'evil' form. Of course these designations are quite problematic from a thematic standpoint, as most spells, with the possible exception of the body rune stat reduction spells, seemed neither naturally good nor naturally evil; it all came down to what they were used against.
After all this shifting and fusing the actual prayers were eventually made available for players to use. If this timeline sounds strange, one should remember that the construction skill was actually listed in the skill list from the very start of the game, with some old world maps even showing a small area in the eastern part of Falador designated as 'player owned houses'. Carpentry remained visible for several months before eventually being removed when Jagex realized that what they envisioned the skill to be simply wasn't possible with the current game engine. It eventually resurfaced several months after the release of Runescape 2 under the new name of Construction, which once again is a name that fits the thematics of the skill far better than the original.
Prayer, as the name suggests, revolves around divine auras that can be evoked to bolster a player's combat abilities and protect them from harm. The skill is trained by consecrating the remains of various slain monsters. This can be done by simply burying the bones (which, for some reason, takes the same amount of effort when standing on a paved road or in the Tzhaar cave as it does when standing in a grassy field), grinding them up at the Ectofuntus or offering them up at their house altars. There are also several minigames which offer prayer XP as one of the rewards.
For a very long time in Runescape Classic, all the highest level players had 122 combat even though 123 was the maximum. This was because training Prayer was both incredibly expensive and insanely time consuming. At the time the game only had two types of bones: big bones dropped by various giants and regular bones dropped by pretty much everything else that could reasonably be expected to have bones. Bat bones were introduced as part of the Merlin's Crystal quest, but they barely provided more XP than regular bones.
To give you an idea of how hard it was to train Prayer in the era of big bones: In Runescape Classic, big bones would give 12.5 prayer XP. This meant that to get the XP needed for level 99, a player would have to bury 1.042.755 big bones. To further demonstrate the insanity of this, you need to remember that noted items didn't exist back in Runescape Classic, meaning that, with 30 bones being the maximum amount that could be transferred in a single trade, a player wanting to buy the necessary amount of bones would have to go through the trade screen a finger-breaking 34.759 times. Even with the introduction of dragon bones the numbers didn't get much better, requiring 217.240 bones and 7.241 trades. Furthermore, the number of quests actually giving Prayer XP could be counted on the fingers of a single hand.
Eventually dragon bone certificates would alleviate the pressure somewhat, but serious updates to the training of the Prayer skill didn't come until Runescape 2. The first serious boost to the training of the Prayer skill came with the introduction of the Ectofuntus as part of the Ghosts Ahoy quest, which was released to the public on February 15th, 2005. On the outskirts of the ghost town of Port Phasmatys players found a ghostly temple with a mysterious fountain spewing ectoplasm, which let players grind up their bones to fuel it in return for ectotokens and Prayer XP at an increased rate of 400% per set of ground bones. While this method definitely increased the speed at which players could train praying, the remote location of the Ectofuntus and the number of steps players had to go through to turn their bones into XP meant that it was still a lot of work.
The biggest boost to the training of the Prayer skill came with the introduction of another skill: construction. From the 31st of May, 2006 onwards, players with level 45 in the construction skill could build their first chapel room and their first altar, with their first incense burners becoming available at level 61. As the quality of these furnishings increased, so did the boosted rate of training they provided to a maximum of 350% for a gilded altar with both burners lit. Even though these new items rapidly accelerated the training of the Prayer skill, they required a serious financial investment. The hundreds of thousands of GP required to train construction up to level 75 would only be the beginning, as the material cost for a gilded altar is well over 1.25 million GP.
These days 9.911 players have reached the 99th level of the Prayer skill. If you had told pretty much any Runescape player as late as five years ago that nearly ten thousand players had maximized their Prayer skill, they probably wouldn't have believed you. However, with the introduction of new training methods, quests with Prayer experience rewards, bones and mini-games with optional Prayer experience, the Prayer skill has long since lost its reputation as hardest skill to train. Achieving level 99 and the achievement cape with its unique angel wings emote is no easy task however, even if it has become quite a bit more common over the past few years.