ERGOT
Linda Caporael's "Ergotism: The Satan Loosed in Salem?", Science, Vol. 192, No. 4234 - April 2, 1976 puts forth a theory on the Salem witchcraft hysteria which suggested that those involved had Ergot toxicity caused by a mold that can grow on rye and has hallucinogenic effects.  The theory was refuted almost immediately by Nicholas P. Spanos & Jock Gottlieb in a subsequent issue of Science.
The basic problems with the theory which Spanos and Gottlieb point out include: 1) specific digestive-tract symptoms of ergot poisoning are not reported in the afflicted; 2) the symptoms would come and go in a group in unison, which is more indicative of a psychological basis for the fits than a biological one; and 3) whole households would be more likely to be affected by a poison in a dietary staple, but only one or two members of any given household were affected.
The theory has a firm place in the current folk theory of the events in Salem, and was used by Robin Cook in his novel "Acceptable Risk."
Both articles from Science are available in Marc Mappen's excellent anthology about how historians have viewed the events in Salem: "Witches & Historians: Interpretations of Salem"  [Keiger: Malabar, Florida. 1996]. This is unfortunately now out of print but could possibly be found through a used bood dealer.

Ergot article

My Take on the Theories
I confess I have not read the encephalitis or moldy rye theories, but I find the idea of the Salem accusers having a neurologic or infectious illness highly unlikely.
First of all, if this was the case, why would it mainly affect only a specific population group - adolescent girls? Further, brain infections/diseases whether acute or chronic, do not present at all the way these 'hysterical' girls presented. People with Encephalitis or
similar diseases or disorders would not be capable of the antics that these girls performed, especially the well timed reponses and behaviors to court proceedings.  Generally people with those forms of illness would be so ill and debilitated they would not be out of bed, and in the 1600's more than likely would not have survived.
Also, the 'seizures' these girls had were not at all typical of 'real' seizure activity which is uncontrollable by outside or inner forces.  Nearly
all seizure victims are unaware of the seizure activity as it is occuring, and are unable to respond in any way to verbal or tactile stimulation.
Someone having a seizure is unable to respond to questions or call out accusations.
Although it is true that some brain illnesses can cause hallucinations, those hallucinations are not of the same sort that these girls were said to
be having.  They would not be well-ordered and well-timed but chaotic and unconnected to outside stimuli.  The hallucinations of someone with a brain injury or disease would not repeatedly focus on one specific event or occurence in other words, but would be multifaceted, disorganized and incoherent.  Affected persons cannot have hallucinations on demand and then carry on with everyday life.
I feel that there were many things going on at that time that caused this event.  Mosts importantly I think it relates to a long standing belief in
divine intervention, current events (including general ill will amongst property owners who were disputing boundaries and control of their town), and the position of children in society. Remember - although it is said that our ancestors came to this country for religous freedom, first and foremost they came for LAND(WEALTH).
By 1692 the old ways were beginning to be questioned by young adults (the 2nd and 3rd generation from the immigrants).  There were some rebellions against the church rule, land owners were feeling the crunch of not enough land to divide among their growing families, town governments were trying to take more control and allow less for the church - even paying and selecting town ministers became an issue. Neighbors were expected to spy on neighbors and report misdeeds to church and town fathers. Their was a tight control on EVERYTHING.  The church and the town meeting controlled all aspects of behavior, and those with the most land and highest standing got the best seats in church and the highest position in government and the military.
There was a heirarchy of control that was well prescribed. The tythingman controlled behaviors in church, town governments controlled behaviors in the town while parents and all others controlled the behaviors of children.  AND all adults were more important, had more voice, and were more recognized than the children ('children should be seen and not heard' attitude).  It must have been very tiring for children -
especially those who were active, imaginative or curious.
So, with all of this in mind and by 1692, after Indian massacres, small pox and other epidemics, church and town discord, neighbors fighting neighbors over land and civil disputes - is it any wonder that someone (especially the children) wanted to SCREAM?
To sum it up, I feel that a bunch of bored (rebellious?), impressionable, pubescent girls were looking for something exciting and different in their lives and got in over their heads.  Perhaps some of the stronger girls had a malicious intent from the start but I think it unlikely. I think they just couldn't find their way out once the adults were involved - and it was easy to fall back on long standing superstitions and blame others who may have been 'different', said a cross word to them, or irritated their parents with a court case.
Once started they could not go back for fear of retribution or being accused themselves, and perhaps there was an element of mass hysteria in some or all as the trials began to get into full swing.
But think how important these girls became!  How exciting each day was in comparison to what they had known in their well ordered lives in which they had been barely recognized. Their lives were no longer a dull monotony that would last until old age and death. They were the center of attention - everything and everyone was focusing on them and their 'afflictions'. Even they could not have envisioned how exciting their lives would become or how long they would be remembered!
As for the adults involved, could they have at first believed the girls were truly afflicted - but later seen how it benefitted them when their neighbors were executed or removed, how easy it was to eliminate their 'problems'?
Divine intervention was the belief that God rewarded those who did good deeds, and punished those who did not.  Every event bad or good that occurred to an individual was 'ordained by God'. It was good vs. evil, paying for misdeeds etc. So, if a cow falls dead today when he was well yesterday, the owner must have done something that displeased God.  Now if the owner could not identify that he had done anything displeasing, then what other cause could there be? AH-HA! Perhaps a neighbor who he was having a land dispute with was a WITCH and therefore she killed the cow in revenge. It easily took the blame and fear off the owner to be able to use someone else as a scapegoat. Old fears and superstitions served them well when grudges, law suits and land disputes were settled by the accusals. Perhaps greed made it easy for them to sit back and allow it to occur, and even prod on their children, their neighbors, their friends - the accusers.
Illness? Infection? Poison?  I, for one, doubt it.