Near the end of the episode "Grave of the Dragon" (before Melfina's put out of commision). After Harry tries to seduce and kidnap Melfina again, he is rebuffed by Gene. As they are about to leave Gene asks Melfina if she wants to leave with him, and that he wont force her to choose. After a few tears Melfina chooses to stay with Gene.
Melfina asks Gene what his wish is and all he wants is for her to go back with him. Not to mention that kiss!
Aisha and Suzuka sneaking aboard the Outlaw Star after they supposedly parted ways with the crew.
Both of the ending themes "Hiru no Tsuki" and "Tsuki no le" count as this.
The very, very end of the series, with the whole crew reunited and setting off for new adventures, both because it's such a good send off and embodies the spirit of Outlaw Star, and because we won't get to see those adventures. The ending caption seals it.