A lot has changed since I reviewed travel websites four years ago. Now the best ones reflect the new realities of travel, and offer to include luggage fees in fare calculations. That helps because $15 or $25 applied each way can turn a good deal sour.
My verdict this time: I found TripAdvisor slightly better than Kayak and Bing Travel...
...I also liked TripAdvisor's tool for calculating bag fees and other add-ons. Simply enter the number of bags you are checking, whether you are have an elite frequent-flier status (which sometimes comes with free bag checking) and whether you'd like to buy food, alcohol or headphones on the flight.
TripAdvisor estimates and adds the fees to your base fare for comparison. A JetBlue flight might suddenly come out as cheapest because it lets you check one bag for free.