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A particular space pirate log entry in Prime, which gives clear orders to all soldiers suffering from phazon-related mutations to report to the authorities. Mutations beneficial to combat are rewarded with a raise and bigger food rations.
There are some fairly hilarious Space Pirate logs you can scan if you look hard enough. The most famous one, by far, is the one that reads:
"Science Team still believes that the Metroids can be tamed. After three cycles of trying and twelve warriors killed, I now believe that Science Team has vapor for brains."
"Science Team has vapor for brains" quickly became a meme among Metroid fans.
"Metroids are not pets. Metroids are not for target practice."
"Unauthorized feeding of Metroids is STILL strictly prohibited."
This is apparently a big problem for the Pirates: you can scan one Metroid in their base that is moving a bit slower than the others; the scan determines that it ate a pet treat and has indigestion.
One of the logs in Mining Station A of the Agon Wastes is about a Pirate grumbling about how all the trips to Dark Aether are draining their power. He then mentions how maybe Command will listen once the power latrines run out of energy.
Injury Report 07.200.07 Unit 686 released a Metroid for target practice today: the Metroid then assaulted 686. He should be regaining brain functions in a cycle.
A log in the Phazon Mines talks about trying to capture Samus' ship. Scientists predict that the ship has a cloaking mechanism so advanced, no one will be able to find it unless by dumb luck. In reality, Samus' ship is in plain sight in an open area a couple of rooms away from some aerial pirates, although this fact could potentially be written off as the cloaking device working on everyone but Samus. Even in that case, however, it'd still be difficult to not notice the rain suddenly stopping in midair...
Even better, this wmg comment in youtube. By the way, great video.
Sven Hallgren: I think it's even more fun to combine the previously mentioned lack of discipline and obvious morale damage from knowing The Hunter is planetside with their inability to detect Samus's gunship. That entire log entry has an air of "Oh no, we DEFINITELY can't find that Gunship that's right over there because going there would end with us splattered on the walls, please buy my story" about it.
"Aran's Power Suit technology remains a mystery, especially the curious Morph Ball function. All attempts at duplicating it have ended in disaster: four test subjects were horribly broken and twisted when they engaged our Morph Ball prototypes. Science Team wisely decided to move on afterward."
A pair of logs side to side in a save station are rather droll for a group of ruthless pirates.
"All Holo-technicians report to Main Observatory. Maintenance required on both holomodules."
"Chief Astrogation Officer feels our current dual holoprojector system is obsolete. Please review and advise."
Omega Pirate's death. You shoot him, he slumps and collapses on top of Samus.
After finally defeating the Chykka, a boss that just keeps getting back up when it seems defeated, scanning the corpse will give you a long list of information about the body's condition that basically amounts, "Yeah, it's down for good now, don't worry."
Bioscan complete. Target Chykka has been terminated. Lifesigns are at flatline. No regenerative ability in effect. No evidence of symbiotic corpse possession. Resurrection does not appear likely.
Metroid Prime 1: After the battle with Thardus, as Samus is turning to walk away, a small rock smacks her in the back of the head. (It conveniently makes her turn around and see a brand-new powerup!)
Go shoot a light beacon with the Annihilator Beam. Watch any Ing in the room gleefully gallop/fly to their death.
Admit it: At the bottom of the Phazon Mines in I, you got a sadistic chuckle out of unleashing a swarm of Metroids on the Space Pirates.
There is also a moment in the Phazon Mines where the player sees a missile-destructible grate on the ceiling. Naturally assuming that there is a powerup stored behind there, the player blows it up... And inadvertently kills the shadow pirate who had been hiding behind it to ambush Samus.
The amazing stupidity of how the Triclops/Mechlops will eat Morph Ball Bombs is considered by many to be amusing. Nearly every instance of the mob AI being Too Dumb to Live could be a CMOF.
Admittedly, the idea is that it tries to suck in Morph Ball Samus and the bomb gets sucked in instead. It's still funny to imagine them having an Oh, Crap! moment just before the kaboom...
Since they'll grab them if you are out of their range, it makes it seem as if the Triclops are simply too stupid to discern between the Morph Ball and a bomb.
For some, Meta Ridley's death, in which several Chozo Statues come to life and blast him with Frickin' Laser Beams. Then he falls into the Impact Crater and explodes! The latter is possibly justified by Meta Ridley being a cyborg.
There's actually a bit of foreshadowing early on when you find a Chozo Lore entry (Log name: Statuary) that basically says "If you destroy our relics, you'll regret it." During the fight with Meta Ridley, his attacks start destroying statues, so he had it coming.
Those who respect and honor these relics will know the friendship of the Chozo. Those who deface or destroy them will know our wrath, unfettered and raw.
Samus also gets a few dozen CMoAs for STILL BEATING HIM A BUNCH.
Metroid Prime 2 reveals the biggest weakness metroids have after the Ice and Dark beams: doors. Whether intentional or a glitch, metroids, for no reason, will explode if they try to enter through an open door and enemies aren't programmed to go into other rooms anyway.
Quadraxis in Prime 2. Remember how his head was bouncing all over the place when you killed him, then it just kinda skidded to a stop in the background?
Or the Space Pirate log in Prime 2 when they realize that Samus and Dark Samus are two separate beings. The reaction is basically, "Oh, Crap!, there's two of them?!"
Scanning Space Pirate Crates in Prime 2 gives us the gem "Space Pirates, strangely, dislike theft." It's even funner when you realize that most of the opinions expressed in non-lore scans are Samus' own, so she's the one making that sarcastic remark.
M. Angseth, Samus Aran fangirl.
PFC Crany: Last night at chow, Angseth starts talking about some bounty hunter and how she blew up a planet full of Space Pirates. I told her I didn't believe in fairy tales like that, and she took it personal. I just find it hard to believe that one person took out an entire Space Pirate base, that's all. But if she wants to believe in this Samus, or Bigfoot, or Santa Claus, she can.
For the sequence breaking-savvy people out there, if you acquire the right equipment upgrades before triggering the boss fight with Rundas, you can defeat him with a freakin' elevator. No, this is NO JOKE...! (x2 speed is preferred) A modified Youtube user comment fits quite well for this hilarious occurrence.
Rundas: You can't defeat me, Samus. My phazon will destroy you.
Also in Prime 3, Gandrayda has a chance of tripping when you fire a powerful attack at her during her boss fight.
Some of the Prime 3 Pirate logs.
"Our scanners have detected the remains of Dark Samus, who has revived herself within our Phazon storage. Surely, we are cursed."
"After our liberation, she (Dark Samus) left us adrift. We thought this a test of our loyalty, and so we endured. Some said she abandoned us. They were promptly shot. Disciples do not doubt their leader. "
It gets better.
"As we groveled in awe, she ordered us to follow the beast through a rift in space, a wormhole. Some refused to follow, afraid of the unknown. They too were shot. Disciples must be fearless."
An unused log in Prime 3 indicates that some of the Galactic Federation marines referred to their Aurora Unit supercomputer brain as the Other Brain, which did not please Admiral Dane when he heard about it.
When Samus obtains the X-Ray Visor in 3, she turns to the screen and gasps, as if she can see the player through the fourth wall.
wmg comment in youtube. By the way, great video.Sven Hallgren: I think it's even more fun to combine the previously mentioned lack of discipline and obvious morale damage from knowing The Hunter is planetside with their inability to detect Samus's gunship. That entire log entry has an air of "Oh no, we DEFINITELY can't find that Gunship that's right over there because going there would end with us splattered on the walls, please buy my story" about it.