I'm pretty much a total noob here, but since no one else has replied yet and I am in the middle of a similar search myself (for commuting in Philadelphia), I'll toss in my $0.02 about the bikes I'm considering.
I'm looking mostly at "performance hybrids," or basically flat bar road bikes. These are essentially road bikes with flat handlebars vs. the drop bars typical of road bikes (for a more comfortable upright position and somewhat better visibility [of the rider, by motorists] in traffic), and generally somewhat thicker tires (range of roughly 28mm to 35mm). Because I may be commuting in less than ideal weather and in traffic, what I've read so far is making me lean toward disc brakes rather than the more standard V brakes, for enhanced stopping power. I honestly do not know if that is really necessary, but I've decided it's a preference... It does make the search a little tougher, and disc brake systems will generally add a bit of weight and cost to the bike. I'm considering models like the Bianchi Camaleonte 2 and 3, and the Trek 7.4 FX Disc.
Other stuff that has caught my eye in the performance hybrid class would be the Fuji Absolute line, Specialized Sirrus, Giant Escape, Cannondale Quick, etc.
I was originally very strongly leaning toward more of a "comfort hybrid," which would tend to have slightly fatter tires (35 to 40mm) and perhaps a suspension fork in the front to absorb shock from potholes and ride more comfortably on dirt trails. Check individual specs, but most of these bikes have a lockout mechanism on the front suspension to make the fork more rigid for riding on pavement. I've decided I just don't like the idea for my own riding purposes. The lockout element just makes me nervous (maybe for no reason, I really don't know) because it *seems* like you go through all these engineering gymnastics to assemble a good bike, and then whatever that tiny lockout mechanism actually is (I don't quite understand the mechanics of how flipping a switch actually prevents a spring from springing) is really the entire front fork while it's engaged - with a chain being only as strong as its weakest link, etc. But WTF do I know? I'm just an unfrozen caveman.
