The Robot Buddy 005, 006 and 007 become friends with in the episode "Mystical Island".
The Christmas Episode involving 003. She's stuck with a needle that makes her enter a waking dream-state, and starts seeing her long lost brother Jean Paul, who was an Ace Pilot. Eventually 009 gets worried and goes looking for her. He eventually does, and saves her from certain death... but not without the help of a strange old airplane that leads him right to her... makes you wounder, don't it?
The bittersweet final sequence of the chapter "The Two Universes": In the year 201x, the Earth is shown at peace. Or rather, a perfect and peaceful copy of Earth, existing in the "universe of light". Jet, Albert, G-Junior, Chang, G.B., and Pyunma appear as normal human beings that are enjoying a day at the beach. They then reunite with Joe and Francoise, who have also been reborn into ordinary human lives. Although Ivan is absent in the manga version, the light novel states that he's there too. The 00 team have achieved their wish for peaceful existence through sacrifice.
Archaia graphic novel
Pretty much any moment between 003 and 009. Most notable are her offering to talk to him to help him deal with their kidnappings and saving him from 0010. Also, after 009 and 002 survive their fall back to Earth, 009 wakes up to find 003 sitting with him in the beach house the cyborgs are now hiding in.
When Joe gets a chance to confront Kai about ordering a hit on him, all he does is demand that Kai leave his sister to live her life however she wants and stop interfering.