It's small, but after Jessica gets irritated at Jay for questioning her in Entry #31, her voice becomes softer when asking him if he's alright, clearly concerned for his well being, despite not knowing him.
In Entry #32, when Jay finally agrees to come clean with Jessica, and tells her to leave her door open. It just feels like he cares about her personally, as opposed to just an asset against The Operator and whatever is influencing both of them.
Then, in Entry #52, he tries to protect Jessica from the Operator by tackling him. Granted, it doesn't work, but it's the thought that counts.
And at the start of the entry (in what Jay believes will be his final message to his viewers), he declares that if Alex tries anything, do he will whatever it takes to make sure Jessica gets out alive.
Entry #61: Tim has disappeared after becoming Masky again. Jay, thinking he knows where Tim is, runs off in the middle of the night to try and save him. Made even moreso because the last time they met, Tim assaulted him and told Jay to leave him alone.
As of Entry #62, it seems that Tim is fine with talking to Jay again provided he's not in his Masky persona. At the very least, he's not screaming at him.
Going off this, Jay's latest tweet, in its own way: "Tim and I are both okay. I'm pretty sure he's going to help me now."
In Entry #63 Jay finally enters some kind of alliance with Tim to get to the bottom of things. His one condition for helping Tim? For Tim to help him find Jessica
Also, although he acknowledges that it does him little good at this point, Tim thanks Jay for returning his medical records.
At the beginning of the entry, Tim also thanks Jay for helping him get out of the woods in one piece (though he refuses Jay's offer to drive him back to town).
In Entry #64, both Jay and Tim risk death to protect the other: Jay tries to help Tim through his coughing fit, and tries to drag him to safety when the Operator appears, and Tim insists that Jay leave him and save himself even as the Operator is approaching.
In the end, Jay finds Tim alive in his car, only for Tim (who is obviously suffering from "Slender sickness" and possibly stuck in Masky mode) to give him a Death Glare and drive off. Jay, realizing that Tim isn't well, closes the video by proclaiming that he's going to find him, vowing not to lose track of him again or let anything bad happen (especially with Alex still out there somewhere).
Entry #65: Nothing in the entry itself, really ... but the sheer emotional response of the MH fandom on Tumblr is practically awe-inspiring. Especially where Tim was concerned. So much genuine fear and compassion (refered to as "Tim Feels") all on Mr. W.'s behalf, despite him being a fictional character. Proof positive that Marble Hornets has not only struck a cord, but has created a very devoted following.
Entry #66: After the incident in the previous episode, Tim begins to wonder if he's really like Alex. Jay disagrees, and though he's clearly not the most skilled person to deliver a pep-talk, it's something.
More than something—Tim actually laughs when Jay says "you're not pointing a gun at me right now." Tim never laughs. But he did.
Just the way Tim says "That's it. No more secrets." Given his personal background (and the events of recent history), the fact that Tim is willing to trust Jay so completely is pretty touching.
Not in an entry, but Tim Sutton asking his fans on tumblr to help him with kicking his smoking addiction. The support he's getting is beautiful.
Likewise, the fan response on tumblr and Facebook after Tim announced the death of his pet rat, Bradley (the same Bradley credited in the Troy Has A Camera videos) was quite moving—particularly the fans who shared their own stories of losing beloved pets.
Entry #69: It's not as noticeable, but the way Jay and Tim speak to each other in this entry, it's lighter-toned than what we've heard from them before. It seems like they're actually starting to trust each other.
The way Jay concernedly asks if Tim isn't overdoing it with his pills (considering what we saw before) and later on, Tim returns the favor by running to Jay's aid when the latter trips and falls into a hole. There's a real rapport building between these two.
It also seems that he wanted to deal with the Operator first so that Amy wouldn't be in danger. Too bad it only works for a while.
Entry 72 shows just how much the relationship between Jay and Tim has grown. As the two of them approach Alex's old house, Jay laments that his memories of the area are so unreliable (as evidenced by the last entry); Tim reassures him that he knows how hard it is dealing with amnesia, reminding Jay that they're in the same boat. Later, Tim expresses concern that Jay may be having hallucinations of the Operator, and (recognizing warning signs similar to his own mental illness) insists they take him to a doctor as soon as possible.
Later in the entry, as Jay and Tim are running from the Operator, they become separated. Tim runs around frantically calling his name, much as Jay did in Entries 62 and 64. He eventually finds Jay laying on the ground, barely conscious...only for the Operator to appear again. He forces himself to walk towards the Operator and tries to stand, seemingly defiantly, putting space between the creature and Jay. Then, as soon as the Operator leaves, Tim runs over and helps Jay get to his feet and back to the car.
It has also been theorized that the reason Entry 72 doesn't have the normal opening and closing text narration is because Jay was recovering and Tim posted it, along with the Twitter update. Compared to how Tim treated him only a few entries prior, it really is heartwarming to see him so concerned about Jay.
Note that when Tim is helping Jay up, he tells him "Stay with me, buddy." Yes, it's spoken in the heat of the moment, but it's the first time Tim has ever referred to Jay as a friend.
Entry #76: Hoody stood guard over Jessica until she woke up, then tried to protect her when Alex attacked them.
Though mostly a Tear Jerker just because you know how it all ends, Entry 84 was heartwarming simply because Brian carried that tape with him all that time. As cold blooded as Hoody was, he still remembered what he used to be like.
Within the tape, we see that Brian was always a nice guy; taking care of Tim, encouraging him to break out of his shell and get involved with Marble Hornets in the first place, and seeing Alex's loneliness and inviting him to join them for dinner.
The Reveal of the origin of Tim's glorious sideburns: Alex said that he envisioned Tim's character having some kind of facial hair, prompting Tim to grow them out. Him keeping them all these years shows that Tim was hanging on to memories of a much happier time in his life.
All throughout their fight, Tim still tried talking Alex down and offer his help. Wow.
In an out-of-story example, the creators have begun selling charity bracelets that donate to the Brain and Behavior Research Foundation. While it's not surprising that they care about such research given the respectful treatment of Tim's mental illness, it's heartwarming to see them be proactive about it.