Ted and John's fistfight...if you think about it, they were the best of friends and they never fought, and although their fight is Played for Laughs, it's hard seeing two best friends fight.
When Lori breaks up with John.
Even worse, she doesn't even give him a chance to explain himself!
When Ted speaks with Lori and offers to leave them alone forever if she and John make up. From her face, you can see she is moved at the living toy making the ultimate sacrifice and wishing things haven't come to this.
Ted's Disney Death. For a while, you really don't think he'll make it.
'She's your thunder buddy now...'
Adding to that, the moment that John gives up hope of bringing him back. He and Lori just sit there for a bit over his fallen Thunder Buddy, and as she tries to console him, there's a THUNDERCLAP.