Question: 
Tonight, over dinner, we started to discuss why a flight from SFO to
JFK is almost 30 minutes shorter than a flight from JFK to SFO. There
were some theories tossed out -- because of the earth's rotation,
because of wind, because of plane routes... I'd like to know the
answer (it was also brought up that flights from Asia to SFO were
shorter than flights from SFO to Asia...) for why time for travel
varies by direction...

A good answer will address: 
- what direction the earth rotates, and how it impacts travel 
- a definition of the "westerlies" "easterlies" and other known
winds...and if they impact travel -- and how these winds move...(this
came up in the debate, it may be that these winds aren't relvant and
that there are other winds that are relevant)...i'd like to know
- do plane routes have any impact on travel times (and what kind of
impact) and what is the governing board that determines international
flight patterns...
A *tip* will be given for a high quality and complete answer.

These answer most of your question:
http://www.aerospaceweb.org/question/dynamics/q0027.shtml
http://www.physlink.com/Education/AskExperts/ae156.cfm

You can blame the earth's rotation, because the earth's rotation
causes the wind patterns.

Around the equator, there's a rainy, windless area called the
doldrums.  Moist air rises.  Just north of the doldrums are the trade
winds that blow from the east/northeast ("easterlies").  North of the
trade winds are a windless dry area called the horse latitudes.  Dry
air sinks.  Old sailing ships got stuck in the horse latitudes and
didn't have enough water for the horses.  North of the horse latitudes
are the "westerlies" which are kind of the opposite of the trade
winds.  The westerlies are the wind that blows across the United
States.  North of the United States, there's more wind, but it's just
blowing across a whole lot o' nothing.