ITA is probably the best at showing the real cost for a number of different fares. As pointed out earlier, EF doesn't show taxes/fees, which can be quite high. A lot of the discount online ticket sellers that you might see via kayak.com only sell non-refundable, non-cancellable tickets, so beware, although kayak itself is pretty good about showing fare codes when it can access them. Orbitz.com is the best of those sites for letting you see the actual fare codes before you try to book.

The problem with AA.com is that it will only show you one coach fare class for an itinerary, and you may want another one if it's available. Sometimes I've had to call to get a fare class changed to one I wanted after first putting a rez on hold. (This is esp. important if AA.com will only give you Q fares for TransAtlantic flights, which are not changeable, not upgradable, and earn zero EQM, EQP or RDMs)