All In One Sites

These sites are great for one stop shopping, allowing you to book the flight, hotel, and car rental all at once. Try booking them together, and separately to see if you're saving, and how much. Start with the "Big Three."
Travelocity
Expedia
Orbitz

For discount airlines, like JetBlue, search on
Sidestep
Best Fares
Kayak
Booking Buddy
Travel Web

Consider "blind" travel sites where you book the flight or hotel, and then they tell you exactly which one for good deals.
Hotwire
Priceline

Not sure how much to bid? Look at Better Bidding.