Alex's birthday present for Marty's 10th is an Alex snowglobe. Although Marty seems to not appreciate it, he then sets it down with 8 other pieces of Alex merchandise, one of them being a picture reading "Happy 7th Marty" making it clear that these are all different birthday gifts from Alex that Marty has kept safe.
When Alex approaches Marty and it appears he's going to eat him, he whispers to Marty thanking him for not giving up on him and asks his friends to play along to help him scare the fossa away.
"It really isn't the fun side without you."
From the Second Film
In spite of their earlier argument, Zuba rushes off to help Alex once he realizes his son went to find the water source on his own. Then when both lions are cornered by the humans, Zuba is truly amazed by how well Alex dances and decides to join in.
Alex: Dad, what are you doing?
Zuba: I'm dancing with my son!
Melman deciding to profess his love for Gloria - through Moto Moto. It really shines through that Melman is the one who loves her, not the shallow womanizer Moto Moto is.
Melman: No, no that's not it. Listen Mototo, you'd better treat this lady like a queen. Because you my friend, you have found yourself the perfect woman. If I was ever so lucky to find the perfect woman, I would give her flowers every day. And not just any flowers, okay? Her favorites are orchids. White. And breakfast in bed. Six loaves of wheat bread with butter on both sides. No crusts. The way she likes it. I'd be her shoulder to cry on and her best friend. And I'd spend every day trying to think of how to make her laugh. She has the most... most amazing laugh... (finally looks over to Gloria, who is in pure awe) Well I mean that's-that's what I would do, if I were you. But I'm not. So you do it.
The other hippos in the pond gush over Melman's confession.
Melman's offers himself as the sacrifice to the supposed volcano God, partly because it'll be a quick way to go, and mostly because maybe there's a chance of getting Gloria water. Gloria quickly tries to talk him out of it.
Melman: Gloria, I just want you to know back at the zoo, it was never the doctors or the prescriptions that kept me going. It was always you. Seeing you every day: that's what kept me going.
Gloria: "This is crazy. I had to go halfway around the world, to find out the perfect guy for me lived right next door."
Alex reuniting with his parents when they get to Africa.
In the ending credits: For our friend Bernie Mac, thanks for all the laughter.
The whole "Trapeze Americano" scene where Alex clumsily creates a spectacular trapeze act with Gia largely by accident to a beautiful song, "Love Always Comes As A Surprise," as they fall in love.
Pretty much whenever the two are on a trapeze, they both have this smile◊ that screams "I'm doing what I love, I'm doing it with who I love, and nothing could feel more perfect than this moment."
The Tightrope scene with Melman and Gloria. It's just pure love right there. At the same time, we see Stefano flying through. Marty's previous scene with his joy flying in the air. It certainly helps that Dreamworks Animation always have a way to make you feel like you're flying alongside him.
Finally, there is that moment when the Zoosters made it back to the gates of the Central Park Zoo, only to discover that they've changed too much to return to captivity. Marty apologizes for putting the gang in this situation in the first place, but Alex tells him that there is nothing to forgive since being sent to Madagascar was actually the best thing that could have happened to them.
It's the way Marty's apologizing that really pushes it home.
Marty: Guys... I'm sorry I ever left the zoo in the first place.
Marty: Because if I hadn't left... we wouldn't have anything to be sad about right now.
Alex: Leaving the zoo, was the best thing that ever happened to us.
Alex: Yeah, out there we were really living it.
There is also how Alex says "the best thing that's ever happened to us". Back in the first movie, he tells Marty that being shipwrecked on Madagascar was not the best thing that's ever happened to us". But after all the adventures they've had before reaching the zoo, it becomes a nice Meaningful Echo.
The fact that the main circus trio are quick to forgiving the Zoosters for lying to them and want them to come back. When they learn from Julien that DuBois have captured the Zoosters they waste no time going to try and save their friends and convincing the rest of the circus to pitch in.