We are actually flying Philly-> Budapest, Krakow -> Philly June 23-July 6. We paid $1140/seat (less $50 for getting the Expedia MasterCard, thus $1,115)) on Expedia last month As I am a tad compulsive I've checked since then not only do our combos no longer exist, but also anything now out there is higher, unless we would have wanted to lengthen the travel considerably by flying through Toronto or such., and that actually saved little.
If it were convenient for you to fly our of JFK I had noticed that Air Berlin had a great JFK-Berlin price, and if you could get the necessary budget connectors to and from there without expensive layovers this could save upwards of $200 per total ticket, although I no longer remember the specifics. I seem to recall also that there is direct and cheaper Lot from Newark to Warsaw, but then the savings start to disappear with the additional connections. For us, living just outside hilly, a transfer to NYC makes no sense. BTW, how are you going between Budapest and Krakow? We took a gamble that the Friday afternoon Orangeways bus from Budapest would be running then, their schedule is only up through the end of March. For some reason, when i asked they would not give info as to whether that Friday PM bus is standard on their schedule. If thta falls through then our costs go up as there is no cheap nor direct flight between these two cities, and we do not want an overnight train.