Booking Buddy just seems to give you the ability to enter your travel information once, then check individual sites one at a time (click on Expedia to see what their prices are, then click on Orbitz to see what their prices are, then click on Delta to see...) instead of having to link to each site individually. Ultimate Fares seems to quote ONLY the base price for tickets - not even including the taxes in the airlines' own 'base' quotes. I just tested it: For an American Airlines itinerary (BOS-MCO, depart 9/29/06 return 10/5/06) for the identical flights, Ultimate Fares' price was $278.10; American's own price was $247.10. I mean, really - $31 service charge? Yeah, right!
Anyway, not that you asked, but kayak.com is a great travel search engine. They even search JetBlue fares, and as solely a search engine, they don't charge us anything, they make their money from the service providers when we link to a site through Kayak and ultimately make a purchase.