Scattered between Honolulu's beaches are several marinas housing hundreds if not thousands of watercraft. LOST made good use of these areas during the series run. "PRODUCTION VALUE!" as the kid in Super 8 says.
The iconic photo of Desmond and Penny that appears several times uses a Honolulu marina for its backdrop. One of my favourite fake-outs occurs in season 3's Flashes Before Your Eyes when it is revealed that Des and Pen are actually standing in front of a fake marina backdrop in London. This photo has an interesting production history -- when it first appeared during season 2 a different actress was shown in the photo, since Penny had not yet been cast. (The inconsistency was fixed for repeat airings and the DVDs.) The scene in Flashes where the photograph is taken also doesn't quite match up with the original -- is it a production continuity error or a hint that Desmond's flash isn't the same history that he had already lived?
The marina made an even earlier appearance in season 1's Hearts and Minds. It is the setting for a confrontation in Australia between Boone and Shannon's "abusive" boyfriend.
Honolulu stood in for Long Beach Marina in several season 5 episodes -- those that featured Jack, Ben, Sayid, Kate and Sun in the evening, as well as the scenes from the following day where Ben intended to kill Penny but ended up shooting Desmond instead. The latter incident also resulted in yet another Ben beat-down.
The high-rise with the turquoise balconies in the photo below can also be spotted in the screencap that follows.
LOST returned to the marina for the season 6 episode Happily Ever After. Charlie takes extreme (and extremely wet) measures to spark Desmond's awakening.