This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Beast Machines
During "Survivor", Nightscream belittles the rest of The Team for losing the Beast Wars. Rattrap responds with this:
Rattrap: You watch your mouth, junior! I lost friends in that war!
Optimus and Cheetor fighting over the possibility of inacting his plan to obliterate all the mechanical life on Cybertron. It was pretty hard watching two of the characters that got along best during the Beast Wars fighting with each other.
Optimus (and the audiance) learning what really happened to Rhinox.
The real Savage/Noble's death while trying to help Nightscream.
The death of Optimus Primal.
Rattrap's feelings of uselessness early on, which all come to a head in The Weak Component when he botches up a mission; gets chewed out; and even hears his teammates talking smack about him behind his back.
Rattrap: Still think you gotta cover for me?! ...You still wanna CUT ME LOOSE?! ...You never believed in me. Ever.
When Rhinox turns traitor, Rattrap seems to take it to hardest, and trails after him a little bit when he departs. Not wanting him to go.
In that same episode, Rhinox's parting comment:
"Goodbye, Optimus. When we meet again, it will not be as allies."
Cheetor takes losing Rhinox pretty hard, too.
"He wasn't just one of us; he was the best of us."
Rhinox's spark speaks to Optimus, revealing he has died and rejoined the Matrix. Optimus lets out a loud, mournful scream in response.