Jean, I've been thinking about this and as much as I adore the romantic moments we have of the Commander, I always come back to that beautiful kiss between him and Helena at the very end of "The Mark of Archanon". Another kiss that I adore is between John and Vana in "The Missing Link",
but the other kiss in "Archanon" wins my vote because of sheer adorability! So full of hope and promise in their uncertain world.
You are also right about that passionate kiss in "Journey to Where". The sheer desparation of all he's feeling in that kiss that produced tears.
Chance, I also love the kiss that the Commander and Maya shared in "New Adam, New Eve"! Very powerful as they were doing their best to fight against it. It's a beautiful moment and I love the atmosphere of that scene. I also thought of this as it's one of my favorites. (I just wish that scene had been lit a bit better!)
Ultimately, the most profoundly moving moment of all for me is in "The Missing Link", near the end when John knew that he had to leave Vana:
Vana - "What do I do til then? At this moment all I understand is my love for you. I do not want you to leave me."
John - "Then cross the bridge between your world and mine."
Vana - "I do not know how."
John - "With your mind and with your heart. As long as you think of me, feel for me, I'll be with you."
Vana - "I will try. Do not forget me. Do not forget me..."