Dens: Naveen & I built 1/2 of the foursquare prototype here (mostly at the back table near the bathroom). The "mayor" feature in 4SQ came from our buddy Chad making fun of us for camping at that table :)
Percolate: Great place to sneak an iced coffee and a mini peanut butter and jelly sandwich (on baguette no less) while you're walking around Soho. Also a good place to chill and do some work on the long benches.
The Corcoran Group: Little coffee house serving delicious, smokey and memorable brews. Great place to hang out with your laptop and enjoy a cup and a yummy pastry.
Gilt City: Coffee mixology gets as complicated and nuanced as chili in Texas, with Oaxacan chocolate and other surprisingly perfect layers to the good old cocoa bean.