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.
Big Lipped Alligator Mission: There's a mission in Jak 3 where Daxter gets sucked into a computer and has to play a Pac-Man style game to find a MacGuffin. It evidently wasn't supposed to be that much of a stretch, since the character who put him into the computer was one with the computer himself, but Daxter's whole body getting sucked through the screen?
Iron Woobie: Jak, starting with the second game, which opens with him being flung into a strange new place, arrested for seemingly no reason, and tortured and experimented on with Dark Eco for two years. And in the third game, not only is he banished by the same city he saved, but near the end, Damas dies in his arms, right as he realizes just who Damas was.
Magnum Opus: The general consensus is that Jak II is the best in the series, although a significant portion of the fandom as well as many reviewers consider it to be The Precursor Legacy.
Mis-blamed: Many fans hate High Impact because of TLF, even though the game's writers work for Naughty Dog and the scriptwriter is the same one that did the rest of the series.
Most Wonderful Sound: The roar of your Dark Eco maxing out in Jak X. Hell yeah. Also the charging noise of the Wave Concussor.
Moral Event Horizon: When exactly Baron Praxis crossed it is up for debate, but it's widely accepted that he crossed it.
For Jak 3, you easily could replace "Baron Praxis" with "Count Veger" in the above statement, though many point to his gloating to Jak immediately after Damas' death.
That's more of a Kick the Dog, though, but because it's combined with Player Punch, it feels like a crossing. His real crossing point came years before, when he kidnapped Mar/Jak in the first place
In TLF, this is the whole reason why Phoenix does his pirating thing in the first place. He quit his military post in the Aeropan air force because it was the Aeropans who, apparently, started the hideous, mind-altering Dark Warrior Project that Haven later picked up.
Even better, the source of dark eco that Aeropa used to fuel the Project was none other than the huge crystal core of their planet, meaning that they were destroying their entire world in the process.
As for Erol, there are only "two words" that can describe that he's crossed the line: " I win, Jak!"
Metal Kor's first appearance. First, this unseen, deep voice says, "Finally! The last Rift Gate has been opened!" and several freaky creatures that look like giant insects come through the portal, followed by some HUGE beast that roars loudly and says, "You cannot hide from me, boy!" I'm pretty sure anyone would shit themselves if something like that happened to them.
Dark Daxter, contrary to earlier reports, doesn't talk like the Hulk and seems to be of his usual intelligence. What makes this fit the trope is that Daxter is genocidal and bloodthirsty while dark, but everything he says sounds frighteningly in character.
Aww, I broke this one. Still hungry—time for more meat-snacks!
The boulder chase in the Tomb of Mar in the second game that at first seems to be a Shout-Out to Crash Bandicoot. What really takes the scare factor Up to Eleven is when a giant spider comes out of the bolder.
That One Boss: The 4th to last boss in TLF (that Deep Purple monkey thing), that can use blue eco to slow down time just like you. Chances that you'll not notice this the first time are quite high. And even when you'll get it, the boss will still be very hard to take down.
They Just Didn't Care: Possibly the reason TLF's story wasn't on par with the rest of the series, despite having the same writers.
What Do You Mean, It's Not Political?: Jak II was claimed by some to be a thinly veiled protest against the 2003 invasion of Iraq and the Bush administration (as supposedly represented by the MetalHead War and Baron Praxis respectively), particulary accusations that that they are wars that were fought solely for political and/or economic gain by governments that had illegitimately gained power.note With Baron Praxis's usurpation of power supposedly paralleling the Presidential election of 2000 There is no proof of that Naughty Dog had any sort of political agenda when they made the game and for that matter had been in development well before the controversies regarding the Iraq War began.