These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Are we listening to Gordon's Inner Monologue throughout the entire series, or is he actually speaking out loud?
On the one hand, the people around him don't usually react to the more outlandish things he says. On the other hand, he mumbles while underwater as if he is trying to talk through his closed mouth.
Gordon concludes that a Mengele-like scientist is trying to send everyone in the world to Xen to die, hence all the dead bodies of researchers.
Awesome Ego: Freeman has started to think very highly of himself, but considering what he's survived, you can't blame him for getting a big head. Thankfully, his brand of egotism is entertaining instead of obnoxious.
Episode 27 as to whether people found the pirate-talk to be funny or not.
Episode 47 gets hit hard with this. It's during this particular episode that Ross Scott allowed a friend of his to play around with sound effects from other games and such, and implement them into this episode. Such changes being the different gunfire sounds for Freeman's weapons, headcrab voices taken from Half-Life 2, and even much more realistic explosion sounds for tank fire. While some found these sound tweaks to be decent, others found it distracting, and out-of-place, after having watched the series through stock sounds for 46 episodes. Afterwards, Ross chose to just go back to stock sound completely, but episode 47 ends up leaving the new sound-effects intact; now making it seem even more out-of-place if the viewer feels distracted by the one-off sound tweaks.
The Lambda Core's detour into Half-Life: Uplink; a nice trip down memory lane, or needless Padding? Part of the reason for the controversy was because of the multi-month hiatus between episodes 57 and 58. People were hyped to see how Ross would go about the Portal maze...only to realize that they were going to have to wait a little longer.
While some found the random "backrubs" heard in the background funny, Ross not reusing the line Adrian Shepard throws at Gordon as he jumped into the teleport to Xen was met with some criticism for those hoping that there would be a brief crossover with Shepard's Mind. Ross' explanation for why he didn't go with the line was because he thought that it would be too predictable if it unfolded exactly as how the fans wanted it to.
Crazy Awesome: Gordon. Scott said that he went for a mentally unhinged and quirky characterization because he couldn't see a normal person surviving the events of Half-Life. His more eccentric attributes do indeed save his life a few times. In later episodes, he also gets pretty lax with his personal safety, seeing as how he considers running right past a Bradley through an open killing field while it attempts to hit him with its autocannon to be a completely viable strategy.
Gordon: Alvin York killed dozens of people, and he was a hero! He didn't even want to, he was like me! Am I a hero? Eh, I don't know, I don't think it's very heroic if the only person you've managed to save is yourself.
Dork Age: The hiatus between episodes 44 and 45 is considered this due to Ross Scott's long-enduring battle to break free from Machinima.
Ensemble Darkhorse: The series as a whole is this in Ross' works. Ross Scott used to only create Civil Protection, but it took a long time to make new episodes, mostly due to the time it took to animate everything. So he created Episode 1 of Freeman's Mind as essentially a comedy skit/experiment to give his fans some entertainment in between episodes. After he created the second episode during another lull between Civil Protection episodes, he planned to end it right there, but fans really loved it and demanded more, and now it's one of the most popular machinimas around.
Fridge Logic: Invoked at several points, with Gordon wondering about the state of the rest of the facilities (and why the place is so recklessly dangerous), such as one time if he wondered if janitors had a higher survival rate since they both have rudimentary melee weapons, knowing the layout of the buildings, and had keys to everywhere.
Hilarious in Hindsight: At one point, a dying guard tells Freeman that a tram leads to the surface. Freeman muses over it, saying that so far the guard had spoken in annoying half-truths. He follows the tram-track, and it does indeed lead to the surface.. But not out of Black Mesa.
Freeman constantly lamenting his lack of a grappling hook becomes funnier if you've played Half-Life: Opposing Force, where Adrian indeed gets a grappling hook...that's just a Barnacle that was pulled off the ceiling, and that he'd probably just pass up, anyway. This is even called back in Shephard's Mind when that comes into play.