There's no one place that's going to consistently give you the best prices. Your best bet is to try a site like Kayak or Sidestep. These sites get information from multiple other sites (Orbitz, Expedia, etc.), so it's a way to look at a lot of information in one place. Once you find the best price, be sure to check that airline's web site, because I have found that the airline's web site will sometimes show available flights that the online travel sites won't. Also, if Southwest Airlines is an option where you live, then their fares are only available through their web site.
Baggage fees vary from airline to airline. You'll have to check with each airline.