Some big things that I find work well in the many Game Jams that I've been a part of or organized:
Centralized location: This is important as it allows people to get together and bounce ideas off of each other. It also helps teams get together and games get finished.
Rigid and adhered-to rules (to a point): As with most creative endeavors, the more stringent the situation, the more the creativity comes through (most of the time anyway). There is nothing more intimidating than a blank slate.
Some constrictions could be Time (48 hours is good, one week is alright), Palette, Screen Size, or Theme (most important).
Don't try out new tools: It's hard enough to make a game in a tiny timeframe, but when you compound that with having to learn a new skill set, it makes things really difficult.
Sleep: People think they can skip it, but it really makes your last day of the Jam terrible.
Note
Eric McQuiggan is a founding member of The Dirty Rectangles which has held various Game Jams, makes Flash games at Fuel Industries and is Vice President of the Ottawa Chapter of the IGDA.
Website: http://ericmcquiggan.com/
Dirty Rectangles: http://www.dirty-rectangles.com/
Twitter: http://twitter.com/EricMcQuiggan