Rav Shemuel Pinhasi (contemporary), in his work Ve’chol Ha’haim (p. 31; listen to audio recording for precise citation), discusses the situation of a traveler who completes a long journey (72 minutes or longer) but has not yet arrived at his final destination. He uses the example of a passenger who flies from Israel to the United States where he is then connecting to a flight to South America. Rav Pinhasi writes that a traveler in this situation does not recite Birkat Ha’gomel until he arrives at his final destination, in South America. Even after he completed the long journey from Israel to North America, and even if he has a layover of one or two days, he does not recite Birkat Ha’gomel until he arrives at his destination.
The reason for this Halacha is that in Birkat Ha’gomel one thanks Hashem for bestowing upon him "Kol Tob" ("all goodness"). One thus does not recite this Beracha until the completion of "all goodness," meaning, when the process is complete, which occurs only once the traveler reaches his final destination.
The exception to this rule, Rav Pinhasi adds, is a situation where the layover extends for three or more days. In such a case, given the length of the layover, that location is considered a destination, such that Birkat Ha’gomel is required. Rav Pinhasi cites this ruling from the Hid"a (Rav Haim Yosef David Azulai, 1724-1806), in his Mahazik Beracha (219:5).
Rav Pinhasi notes that one recites Birkat Ha’gomel upon arriving at his final destination even if he stays there for only a brief period, such as a day or two. Since he arrived at the place where he wanted to go, he recites Birkat Ha’gomel, regardless of the duration of his stay. Rav Pinhasi (in footnote 9) cites this ruling from several Halachic authorities, and notes that this Halacha applies to "Sheluhim" – representatives from Israel who travel to many different Jewish communities throughout the world. Even though the "Sheluhim" spend only a brief amount of time in each location, they recite Birkat Ha’gomel upon their arrival at each, since each constitutes its own destination. This is also the ruling of Hacham Ovadia Yosef, in Hazon Ovadia – Hilchot Berachot (p. 364).
Summary: A traveler recites Birkat Ha’gomel only upon arriving at his final destination; he does not recite Birkat Ha’gomel during a layover, unless the layover extends for at least three days. Birkat Ha’gomel is recited at the destination even if the traveler plans on remaining there for only a brief period of time.
