Dan's reaction to Masquerade having Hydranoid blast Drago even after he's been defeated. Even worse when Drago is sent to the Doom Dimension.
The death of Masquerade counts, simply for him being so calm and excepting of his fate.
All the kids having to say goodbye to their Bakugan partners.
Drago becoming one with the New Vestroia's core.
Skyress leaving Shun, for the last time. After Shun's been busting his ass to save her.
The deaths of Anubias and Sellon were surprsingly tear inducing despite the fact that the pair showed almost zero redeeming qualities. While Anubias was by far the more sympathetic of the pair, watching Sellon plead to live just long enough to see the perfect world her master planned to create was a very Kick the Dog moment for Mag Mel.
After not seeing many of these Bakugan for years, it was great to see Preyas, Elfin, Tigrerra and the like again. What was not so great was watching them all being slaughtered while trying to defend New Vestroia. It was all pretty horrible, but the death's of Elfin, Amazon, Preyas and Tigrerra were probably the biggest tearjerkers.