Among them, appearances by Astra (the first one (Ep.22) and the Ultra Smackdown (Eps. 38 and 39) are great!), Ultraman King, the Ultra Brothers, Anne from Ultraseven, Fuji and Hayata from Ultraman, and even Ultraseven in a vision.
Also, Ultraman Leo's smackdown vs Alien Magma and the Gillas brothers in Ep. 1.
Ultraman King - he will take you to school and teach all 8 of your classes.
Commander Black getting beat to death by the kids Gen trained. Even more so because Black deserved every second of it.
Leo's Big Damn Heroes moment saving Ultraman Zero, his student, in the Ultraman Zero Gaiden DVD special. There's a reason Zero is such a badass after training with Leo.
Astra's Big Damn Heroes moment in Episode 46 was sweeter because it was the only appearance of his where he singlehandedly defeated the Monster of the Week. Leo was injured, so Astra pushed the kaijuu away from his brother, shrank to human size, and flew in the mouth and out the back of it, blowing it up! He then picked up Leo and both flew away, with a slow version of Leo's own Big Damn Heroes theme from Episode 1 playing in the background, a human father and child looking on. Sadly, it was Astra's last appearance.
From Episode 1, Dan and Gen swear to help each other out to eradicate alien attacks and invasions. The scene is set against the setting sun, after the storm that the Gillas Brothers created had dissipated.