Oh boy, i've heard my fair share of them throughout the years. Many will be Europe-centric, but the one that I saw followed worldwide was not saying "have a nice flight", as it supposedly brings bad luck. Many other expressions have been coined to wish well upon a flight crew instead, from "happy landings" to "tailwinds". This one rubbed off on me just by exposure, so i'll generally just say "have fun". A few other random ones I heard from people I flew with:

• Never pose for a picture with the plane before a flight, only after. You don't want that picture to be used on the news report if something bad happens. I may or may not do this.....
  
• When flying RG Cessna singles (with a notoriously unreliable gear system in public eye), an instructor told me that for good luck in getting the gear to work he would crawl into the gear bays and click the up limit switches a couple of times during preflight.
  
• As a good luck charm, at least in Italy, you would keep the cork from the champagne bottle you open with your class on your first solo flight. During the party, you write the registration of the plane and the date of your solo on it. I still keep mine in my flight bag, more so as a tradition, and to remind me of my early days of flying. It reads "I-AMAT, 10/01/09".