Crowning Moment of Heartwarming: The ending of Solitary Vigil, when Bubbles manages to save Blossom's life and avert the events of Syndrome and Relapse by taking the blade, and manages to warn the Professor to never bring any of them back before passing away. Doubles as a Tearjerker.
Nightmare Fuel: The various deaths, particularly Blossom's first and final in Immortality Syndrome.
Relapse provides even more, including a sickening moment which reveals what happens when someone attempts to resurrect another without all the pieces...
The Woobie: Bubbles, especially in Solitary Vigil.