In the episode "Showdown at the Super Secret Spaceship Hideout", WordGirl and Dr. Two-Brains stop their fighting to think about their old friendship and how it used to be after Dr. Two-Brains discovers the book he wrote as Prof. Boxleitner. After WordGirl says that he was a brilliant scientist before he turned evil, he briefly looks at her with warm sparkly eyes. That made this troper want to say "awwwww".
The episode "Cherish is the Word". Not only does Tobey give WordGirl a chocolate human heart and tell Victoria Best that she's the best superhero, WordGirl even says that he can be her non-enemy. WordGirl/Scoops fans might have been annoyed, but WordGirl/Tobey fans like this troper loved every minute of it.
Err, that was all well and good until Tobey screwed it all by attacking Scoops. Though to his credit, this was the result of a misunderstanding he had involving Scoops and Wordgirl, but it still causes him to not end up Wordgirl's valentine nonetheless.
The episode "Lady Redundant Woman Gets The Blues". Royal Dandy calling Lady Redundant Woman his "mum". Also a Tear Jerker since she destroyed him.
In "The Young and the Meatless", The Butcher treats Dupey like a real person and not just one of Lady Redundant Woman's copies. Later, he's easily able to tell them apart even though they look identical.
The Butcher making peace with his father and playing catch with him in "Meat My Dad".
The Butcher letting the little girl keep his cat in "Meat With A Side of Cute".
In the episode "Where's Huggy?", WordGirl gives a speech about how much she missed her best friend and sidekick. Counts as a Tear Jerker since Huggy (As Bob) and The Butcher cried after it.
Not to mention that WordGirl and CHF hugged for the first time in the series.
In "The Rise of Miss Power", Mrs. Botsford telling WordGirl she is proud of her (bringing tears to WordGirl's eyes) and subtly hinting she knows her secret identity.
Also in "The Rise of Miss Power", right after Tobey's heart is crushed by WordGirl, his robots hand him a picture they drew of him and them together. It's especially heartwarming because the viewers can assume that Tobey really doesn't have any friends that he didn't build himself.
Two Brains coming to Becky's rescue in "A World Without WordGirl".
Mr. Big and Leslie missing each other, and eventually making up in Yes Monkey.