I am curious to know the correct usage of these words as it seems to be misused often. See https://homebrew.meta.stackexchange.com/q/202/59 for a related question.
From Dictionary.com and the Free Online Dictionary: fermenter: any agent or substance, such as a bacterium, mold, yeast, or enzyme, that causes fermentation; or, (also fermentor) an apparatus that maintains optimal conditions for the growth of microorganisms, used in large-scale fermentation and in the commercial production of antibiotics and hormones.
So fermenter can mean either the enzyme or the fermentation apparatus, whereas fermentor can only be used to mean the apparatus.
The -er ending in a word usually designates a person who performs some sort of function related to a verb. For example, someone who fishes is a fish-er. Someone who performs carpentry is a carpent-er. Someone who doctors is a doctor-er, but the extra -er isn't usually used.
The -or ending in a word usually designates a machine or piece of equipment associated with a verb. For example, a machine that processes food is a food process-or. A machine that calculates is a calculat-or.
So, when talking about the fermentation of something, the container the fermentation takes place in is a piece of equipment, or a ferment-or. The person (or organism) doing the fermentation is the ferment-er. The final judge of the fermentation is the drink-er:-)