This site is quick, efficient and usually has the best published price from what I have seen.
http://www.expedia.com

This is always a good place to try and get a deal. I have used them along with the others I will add, have always been satisfied.
http://www.travelocity.com

Hotwire has some incredible deals if you get lucky. I have used them and only had good experiences.
http://www.hotwire.com

Orbitz is a great site for finding deals. I have only done 2 trips with them and found it to be a good fluid experience they have. Functionality is good and worth trying to get your deal.
http://www.orbitz.com

This company is a bit insane with the whole William Shatner thing but it must work because they keep using it. I tried them awhile back and named my own price. I got it, so it was cool.
http://www.priceline.com

Just did some work with these guys. Their platform is pretty cool and seems quite effective.
http://www.kayak.com

Vacation Rentals by Owner
http://www.vrbo.com/

http://www.matttrip.com