The wacky and fun episode of Dexter having to deal with Deedee's imaginary friend hanging out with him ends with Dexter wishing away the imaginary friend, and commanding him to never come back again. And he does. Deedee runs away sobbing. Then it fades to credits where Koosie just laughs and it suddenly becomes Nightmare Fuel.
Dexter is so guilty that he finally gives Koosie the hug he's been wanting the whole episode.
The ending to "Way of The Dee-Dee" with Dexter in his destroyed lab and Dee-Dee running off in tears.
Dad's speech about Pet Heaven in "Filet of Soul".
Mandark's dream at the beginning of "Mandarker".
Dexter's operatic solo at the end of "LABretto".
The episode "Dee Dee's Tail" is about Dee Dee convincing Dexter to turn her into a horse and, as you can imagine, she is very happy... Until she realizes her brother and her friends just want to use her for rides, not caring if she is tired (even when she is lying down after taking her friends to a ride the whole day, all they do is show her a chariot they want her to pull). Realizing that the people you love just want to use you and don't care for your feelings is really sad.
Dee Dee: This is terrible... First my brother and now my best friends... (crying) I wish someone would help me...
As quoted from Fridge Horror: "When watching Dexter's Laboratory, if you think about it too much, you'll realize what a cruel, destructive jerk Deedee really is. When she's not completely destroying her brother's life's work, she at times openly belittles, insults, humiliates, and abuses him for kicks and giggles." You need only look at such episodes as Road Rash, The Big Cheese, LA Bretto, Framed, Sister Mom, Dimwit Dexter... you get the picture.
This is doubly worse when you think back to the few times that Deedee herself is in trouble. You can tell that despite everything, Dexter has some serious Big Brother Instinct going on, despite being the younger brother who gets put through hell by his sister. That says nothing good about Deedee and a lot of good about Dexter.
Dexter's slinking away from his family in Old Man Dexter after being shot down when wanting to spend time with them is treated to a few oddly long shots without any comic gags in them.