When Sparadrap creates his second avatar in Season 2, Omega Zell refuses to help him level up in part because he knows his priority will be to rebuild his pet collection. Sparadrap then replies, on the verge of tears, that all he wanted was play with his friends. The few seconds seprating that from Ystos showing up are quite sad.
Here's one that is possibly unanimous : Roxana killing off Sparadrap's pets in Season 3 finale. While so far, Sparadrap's obsession with collecting pets was used as a running gag to show his Stupid Good persona, this incident is played seriously and counts as a major Break the Cutie.
In Season 4 finale, Arthéon disbands the Noob guild because he considers that it has no reason to be. However, the reason he was able to give the news to all his former subordinates (except Couette) at the same time was that they were all having their respective fights against the enemy in close proximity to each other. That was happening despite Omega Zell having changed guilds and Gaea having changed factions.
The end of the flash-back about Tenshirock's past shows that his "hacker den" is actually Judge Dead's unoccupied room.