One of my players has a character called Alcemides, a Nemedian Scholar belonging to the Cult of Ibis, who has the Craft (Alchemy) and Craft (Herbalism) skills.
Like Darth Mikey suggested, I allow him to make a Craft (Herbalism) check to identify a given plant. I use DC 5 for common everyday herbs (like Sage), DC 10 for exotic or rare herbs that he has worked with before or DC 15 for an exotic or rare herb he knows only by reputation.
If he is trying to identify the plant from it's powder, juice or sap, rather than the dried (intact) or fresh form, I add 5 to the DC.
I use a similar system for analysing alchemical compounds, with the DC for identification being the same as the DC for creation. I add 5 to the DC if he doesn't have enough ranks of Alchemy (and Herbalism in some cases) to actually make the stuff, and usually insist that he has access to his laboratory.
I also use some common sense here. If he were to analyse a sample of the Golden Wine of Xuthal (which he has never heard of), for example, I would tell him that it is a fermented plant extract of indeterminate origin, alchemically treated, and that it appears to have certain regenerative properties, not "its the Golden Wine of Xuthal and it heals hit points and stat damage".
With regard to what existing items he is capable of making, again, like Darth Mikey said, I make him do some research. He either has to reverse engineer it in the lab from an existing sample (I'd allow this for Flame Powder, for example) or else he needs to find the actual recipe during the course of his adventures (as he has done with Acheronian Demon Fire during a recent escapade).
On occasion, he has attempted to devise his own alchemical concoctions (although only one has been successful). At this point, we usually discuss the effect he is trying to attain, I decide the difficulty (usually with an eye towards game balance and whether it fits in with the feel of a Conan story) and have him make a Craft (Alchemy) roll to create a workable recipe.
