While I have no direct personal experience with Bestfares.com to offer, I would like to bring up the caveat that I understand that airlines do not award frequent flyer miles to itineraries bought on Priceline.com and the like (perhaps Bestfares as well?).
My suggestion is to find a terrific travel agent who really knows the ins-and-outs of ticketing, which involves the agent having a terrific relationship with the airlines as well as yourself. This makes the entire process efficient and satisfying.
Bestfares, airline sites, Biztravel, and the like will, I submit, promote only what they have available to promote, which, as mentioned earlier, precludes carriers such as WN. On the other hand, travel agents have the full range of airline, fare, schedule, etc., options to offer you. Whether you fly certain of those airlines available (such as WN or TZ) is another issue, but being able to make as informed a decision as possible is the leverage with which you empowered when working with a good travel agent.
And let's not forget about personal accountability... how many threads and posts are there in FT about trouble with this-and-that online booking website???
P.S. I am not a travel agent, nor affiliated with the industry... but I have benefitted vastly from having a great travel agent, and while I book off the web often myself, running a fare or itinerary by my agent helps me validate that I am making the best decision and therefore getting the best deal.
[This message has been edited by FQTV (edited 06-04-2000).]