Even more so, when they save Otto from the monkeys.
The scene where Otto makes wooden copies of Larry and Tudrussel and calls them all "one big happy family" (with Otto mimicking Tuddrussell and Larry before stuffing his face with sand and salt water). It really shows that he does see Larry and Tuddrussell as his parents and the only people in the universe who care about him (even though they didn't realize he was gone until near the end).
Buck giving the poncho he's sewn in the Alamo prison with the caption "Larry 3K" to Larry ( Before Buck backed away from Larry trying to hug him) in "Forget the Alamo."
Otto's birthday party in "Love At First Flight". The whole thing is unbelievably sweet, especially when Otto hugs Tuddrussel and Larry after opening his presents.
Otto reuniting with Larry and Tuddrussel at the end of "Orphan Substitute," after Otto is forced back into the orphanage and Larry and Tuddrussel are struggling to find a replacement boy genius to help them on their missions.
While even the following dialogue to be sort of sad and bittersweet, Otto begging for forgiveness during the scene is just precious. You just want to give this kid a hug?
Otto: I'm sorry I got mad at you I'll be good and I'll let you win at video games and I'll let you steal my dessert and I don't want anyone throwing me in trash cans anymore except you!
Tuddrussel: Aww, I'd throw you into a trash can any day, little buddy!
Lewis and Clark getting back together in "Lewis and Clark and Larry."
Clark: I've been doing terrible without you! My clothes stink, I don't know where I am, and I'm starving! I neeeed you!
Lewis:(delighted gasp) You don't know how long I've been waiting for you to say that.
"Father Figure of Our Country" has a pretty big one; Tuddrussel gets incredibly jealous of George Washington as the president spends the day with Otto. He treats Otto with more fatherly affection than Tuddrussel could ever muster up, teaching him the things that Tuddrussel had failed at doing and paying attention to his needs. Then towards the end Washington askes Otto if he could adopt him! Otto's overjoyed reaction is just sweet in itself. And when Tuddrussel comes out to challange Washington over who Otto belongs to, Otto has this to say-
Otto: "Wait, you don't understand! I want to stay. (BEAT) But I can't. My place is with Time Squad." Then we get this-
Tuddrussel: Wait, so you're pickin' me over him then?
Otto: "No one could ever replace you, Tuddrussel."
The episode is extremely sweet as that's one of rarest times where Tuddrussel is showing some desire to be a true fatherly figure to Otto, something that he never often openly expressed in the series.
Also, almost every moment where Larry acts as a parent toward Otto, such as in "Forget the Alamo" where he is teaching him how to sew. There's also when he obviously cooked his favorite foods, and during the Sick Episode where Larry is shown telling Otto to put a jacket because it is cold outside, and later in the same episode, taking care of him while Otto passed out on his knees. Compared to the first episodes where Larry was shown aloof toward Otto and only thought him as a nuisance, it is clearly a sign of great Character Development for their relationship.
Speaking of Otto and Larry, one of the best examples of this is when in the third episode,in the beginning of "The Island of Doctor Freud", Otto and Tuddrussel are swapping stories from their dreams the night before. Otto had a dream that he was a robot, and with Tuddrussel to say, "ugh you mean like Larry?" Otto fires back with, "No, not like Larry. A really COOL robot!" Well, fast forward to the next season in "Horse of Horrors" and Larry is depressed that nobody has noticed that it was his birthday. But then Otto comes in with a birthday gift, which was a handmade picture of the robot made out of dried macaroni and glitter with it saying, "Larry is cool" at the bottom of it.
There is also the moment where they are spending some free time in "Kubla Khan't" while Tuddrussel is "busy" with the mission. That's maybe the first moment they share together as parent and child.
In Kubla Khan't, there's this moment where Sheila Sternwell asks Larry who Otto is. Otto introduces himself and innocently brings up the fact that he's from the 21st Century. Larry, shaken up by her presence and not really knowing what to say to her, confesses that he's an orphan and that he and Tuddrussel "have sort of...adopted him." Sheila quips that abduction would be the legal term. But Larry sternly insists he was adopted.
In "Nobel Peace of Surprise" episode, Larry trying to defend Otto. (Though he fails). Keep in mind that most of time Larry is a coward who either runs away for his life or hiding behind Tuddrussel whenever there is a danger. This fact just shows how much he loves Otto.
If you look into Larry's perspective in "Ex Marks the Spot", Larry showed his affections toward Tuddrussel more than he ever did in the series, and while that had his funny moments, it's really clear that he is very afraid of losing Tuddrussel and definitely cares about him.
Also in a more subtle example when it comes to XJ 5. Even though he helped Larry because he didn't like the idea of Sheila and Tuddrussel together, that was kind of nice to see him getting a more protective side toward Sheila despite being The Stoic.
While it's a common occurance for Otto to give the historical figures a "heartwarming" pep talk that changes the person's mind- the time where he talks to Attilla the Hun is really special because this time he's not just saying this stuff to just cheer someone up, he's saying it from the heart from one bullied kid to another.
Attilla: The kids in Hun school were right. I'm just a 'big dummy four eyes.'
Otto: They called you Four-Eyes, too?
Attilla: Yes, all my life.
Otto(BEAT. Otto's sadness turns to anger): You know what? You shouldn't listen to them! You're Attilla the Hun, one of the greatest leaders of all time with one of the most powerful armies the world has ever known. I believe in you, your problem is that you need to believe in yourself!
In a Real Life example, on May 4, 2012 Rob Paulsen's podcast "Talkin' Toons" MarkHamill was the guest of the week. In the interview the very first topic Mark talks about is Time Squad, saying that he had so much fun working on it and how he loved working with Rob and Pamela Adlon and Dave Wasson. He defended it from the snarky comments that called it a "Peabody and Sherman" ripoff, and just spoke so lovingly about it. He had also expressed wishes that it had gained a cult following like the current Cartoon Network show, Regular Show. Then, Rob and Mark just burst out talking in their respective voice roles as Tuddrussel and Larry, which is just hysterical. Their discussion on Time Squad kept coming back within the interview and they both seemed nostalgic and respectful of the show. Realizing just how much the show was ahead of its time, and knowing that these two voice actors who have done so much work within the last 20 to 30 years have such loving memories about it, is so wonderful to know as a fan.