I signed up with bestfares.com which charges a membership fee to get the member deals but there are free deals too. You can also find stuff on smarterliving.com as well as the usual ones like travelocity, expedia, lastminutetravel.com. I usually find the fares on those travel websites and then go directly to the airlines so I don't have to pay the 5 or 10 dollar fee for those travel websites.
I just completed a 2 city trip. I had to buy 2 one way tickets and one roundtrip (b/c it was cheaper than the 1-way). If you are flying to cites covered by Southwest, you can get in on the $92 internet fares (1 way)
I would definitely use priceline for hotels. I got 3 star downtown philly for 38 bucks