Wow, this topic has been eye opening and educational for myself. And I have to get a chuckle out of a poster named "Ugulu the Barbarian" trying to study alchemy. 
Something I thought of in regards to the Philosopher Stone was, it's suppose to be the ultimate object that an alchemist can obtain. So it wouldn't make sense that a level 1 alchemist already has one. But perhaps you could start them off with a "Transmutation Stone" - something that ats like a Philospher's Stone, but is much less powerful. Philosopher Stone is extremely rare, but Transmutation Stones are fairly common.
Transmutation Stones, depending on what field of alchemy the person went into (mid-eastern, far east, european) would turn certain items into certain other items. So for example, the mid eastern route, for level one, you could turn several rocks into a small golem snake, and you could turn lead into copper, and you could create a potion that cured light wounds. The far eastern field would let you create a liquid that could turn some dead branches into a coil of snakes, and let you grow edible plants out of nothing but water, and let you turn a small handful of sand into silver once a day.
The Philosopher's Stone, would be an end game thing, and something the player would have to quest for 20 levels in order to get, but at levels 5, 10, 15, offer up clues as to where it might possibly be. Even then, if you don't want the player to turn it into a major headache at epic levels, you could always say it has only a certain amount of power and must be idol for a certain amount of time after use each day, or you have to go up to the highest mountain and stick it into a sundial of power in order for it to be fully charged again.
Anyways, interesting reading, and please update this thread with your thoughts and ideas. I have an alchemy 'skill' in my campaign, but it is definitely not in depth, and needs more work.

Something I thought of in regards to the Philosopher Stone was, it's suppose to be the ultimate object that an alchemist can obtain. So it wouldn't make sense that a level 1 alchemist already has one. But perhaps you could start them off with a "Transmutation Stone" - something that ats like a Philospher's Stone, but is much less powerful. Philosopher Stone is extremely rare, but Transmutation Stones are fairly common.
Transmutation Stones, depending on what field of alchemy the person went into (mid-eastern, far east, european) would turn certain items into certain other items. So for example, the mid eastern route, for level one, you could turn several rocks into a small golem snake, and you could turn lead into copper, and you could create a potion that cured light wounds. The far eastern field would let you create a liquid that could turn some dead branches into a coil of snakes, and let you grow edible plants out of nothing but water, and let you turn a small handful of sand into silver once a day.
The Philosopher's Stone, would be an end game thing, and something the player would have to quest for 20 levels in order to get, but at levels 5, 10, 15, offer up clues as to where it might possibly be. Even then, if you don't want the player to turn it into a major headache at epic levels, you could always say it has only a certain amount of power and must be idol for a certain amount of time after use each day, or you have to go up to the highest mountain and stick it into a sundial of power in order for it to be fully charged again.
Anyways, interesting reading, and please update this thread with your thoughts and ideas. I have an alchemy 'skill' in my campaign, but it is definitely not in depth, and needs more work.