There are few agencies that give you deals on airfare. There are some ticket brokers out there that may have some deals but many charge additional for their service.
You can use search engines such as Orbitz, QUIXO, to search for fares and get an idea what prices are. Once I find a low price I go directly to the airline's website and I usually beat the price for a few dollars or find a cheaper price. Most third party booking engines, such as Orbitz add a $10 service fee.
When it comes to cruises I RARELY have found that the big boys such as Travelocity or Orbitz cruises can beat many other cruise sources. I did book "once" through Orbitz (National Leisure) for a cruise because they actually did have the best deal. That seems to have been a one time shot.
The key is to shop around. Use some of the advertisers on this site, try Bargain Finder on the Cruisemates Home Page or if you would like to email me I will give you a couple I have been happy with.