cars.com - has some good filters that helps you narrow things down and a lot of vehicles
carfax.com - equally impressive inventory and all listings have a free carfax to look at. This is the site I found my car.
and then there is my credit union's database they tie into here:
http://www.cudlautosmart.com/ASEntry.aspx?cucode=3983 This is where I found my 2011 Odyssey EXL for 6k less than here in Utah. Had to fly out to NY to get it but this site has a ton of listings too.
Craigslist was hit or miss as was eBay motors.