During the "Giegue's Door" segment of Magicant, the playroom flashback montage shows young Giegue rolling around in a white cloth and eventually levitating around the room with it draped over his head, making him look like he is dressed as a ghost. This becomes fridge brilliance when you realize the song that plays during the ending credits is titled "Ghosts in Flight" and has lyrics that sound like they could easily be sung from Giegue/Niiue's perspective. And who is the only vocalist to perform with Nowheretrain during the game? Why, Niiue, of course! And what is he doing when he drifts on-screen during the credits? Singing into his mic! He continues singing until an instrumental break arrives in the song, and then he stops the singing animation, turns into his original self and walks down the screen to join the Applechasers. He's a ghost, all right, just like he remembers from playing as a kid.
Looking into the Apple of Enlightenment drives Giegue even more insane, while it strengthens and guides the Applechasers. Since this apple was created to stop invaders of the Solar System, of which Giegue is one of those invaders, it might have been deliberately designed to have negative effects on his race if they viewed it.
It might be a bit confusing how Zarbol has a name, considering he's Buzz Buzz. But if you look closely in EarthBound (1994), you can notice that he never introduced himself. Ness assumed who he was joined by sound, and Starman Jr. was just being insulting by just calling him by the noise he made because he was a space insect. Zarbol only told the prophecy, nothing about himself.
Ever wonder why Niiue looks like Giegue if he decided to dress up as a human? Niiue represents all the good childhood memories of Maria and emotions that Giegue discarded in order to launch a second invasion of Earth. Another reason why Niiue looks like Ninten from MOTHER (but with blonde hair) is also due to Giegue's memories of Maria, as well as Ninten, who was Maria's great-grandson. Giegue may have briefly felt connected to Ninten due to him technically being family, but that vanished when Ninten rejected his offer to board his mothership. And plus, Ninten and his friends were the sole reason why Giegue was defeated, not to mention Ninten's great-grandfather George's theft of the aliens' knowledge of PSI.
Even the logo has this. The o in Mother seems to be blocked, and the planet that'd normally be there is in Cognitive. Cognitive is in white, while Dissonance is red. Beyond the plot relevance the term has between Giegue and Niiue, the white side of the logo itself foreshadows Niiue having Giegue's memories and love for Earth as well as his purer emotions, while the red side of Giegue's is laden with his power's corruption and breakdown.
The BGM playing in the two Earth towns from Chapter 6, Thunderton and Cloudvale, are EarthBound-style remixes of "Your Lucky Day in Hell" and "Last Stop: This Town" by Eels. While at first glance this appears to be a case of Anachronistic Soundtrack—CogDis takes place in the 1980s, while the two songs were respectively released in 1996 and 1998—their appearance on Earth actually makes sense: these two towns are under the influence of the Pigsnout Society. The Greyface, the leader of the Society, is a time-travelling PorkyMinch. Having grown up in the '90s, it is likely that he had heard these songs before setting up camp in '8X, and thus their presence further cements the impact of Porky's actions on the timeline.
Giegue's influence causes poltergeist activity and drives animals and people receptive to it to aggression. A log entry shows Giegue actually intended to remove emotion from Earth life so that the beings could become logical, and had only aggressive results on any lifeform effected by it. Given that Giegue himself is anything but logical and is driven to insanity trying to control his emotions, it's only natural that his influence would transfer this madness to other beings. His goal was doomed from the start because if he can't control his own emotions, why would he be able to control anyone else's?
During the final fight of the Paradox ending, you face a cute baby Giegue and four strange swirls named "N-Swirl, A-Swirl, L-Swirl, and T-Swirl." Defeating them and taking the loot left behind reveals a red cap, a ribbon, a bazooka, and a sword — items respectively related to Ninten, Ana, Lloyd, and Teddy from MOTHER. Oh no… oh no, no, NO!! And then a Time Crash happens.
There's a reason the Paradox final battle has "Megalovania" playing in the background. Everyothertime that song was used, it was in the case of the hero or player doing something morally dubious (if not unforgivable) when they could have picked a less drastic path. The Paradox ending is the only case in the whole series where you defeat Giygas with brute force, which is totally antithetical to the canon MOTHER games, where the final bosses could (only) be defeated non-violently. And since defeating Giygas this way causes a host of problems for everyone else, it's only fitting that whatever's left of the first game's protagonists would try to stop you.
and Cloudvale