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.
Crowning Music of Awesome: Created by Arata Iiyoshi (aka S.D.D.) & Atsuhiro Ishizuna, each series has many memorable tracks reprising several distinct melodies and themes. Explorers of Sky eventually unlocks a Sound Test where the player can listen to the entire soundtrack (all 141 songs!) at their leisure. Among the picks:
The music that plays in Crystal Cave (Tracks #43 and #44). If crystals could be played like musical instruments, they'd sound like that.
How about Track #59, "Hidden Highland"? It makes a nice dungeon theme, but it is truly memorable for its use during the scenes when Dusknoir warns about being erased from history, and again during Grovyle's special episode for Dusknoir's Hannibal Lecture, and Darkrai's Motive Rant at the end of the epilogue story.
Track #62, "Through the Sea of Time": First heard during the player's entry into the Hidden Land, this piece takes on a new meaning when it emotionally punctuates Grovyle's Heroic Sacrifice against Dusknoir. Track #63, "In the Hands of Fate", which reprises the same melody slowly and solo, is also heard a precious few times.
Tracks #70 and #72, "Don't Ever Forget..." and "Farther Away...", could be the single most emotional theme in the entire soundtrack, considering that it's heard only after defeating the Final Boss, right as the change in history erases the player from existence, leaving the partner to return home alone.
Demonic Spiders: Pokémon with multi-hit moves in general. Octillery is probably the best individual example of the trope—it packs Bullet Seed, which hits multiple times from a distance, among other things.
Any enemy with moves that hit an entire room. Nidoqueen with Earth Power and Ledian with Silver Wind WILL make you tear your hair out.
8.8: The fans were not happy about some review scores, particularly the 3/10 Game Informer gave Blue Rescue Team.
Epileptic Trees: The Decrepit Lab is solid evidence that there used to be humans in the world where Red/Blue Rescue Team takes place. The unanswered question is... what happened to them?
Human civilization suffered an extinctionary catastrophe thousands of years ago and the story of Red/Blue Rescue Team takes place in an "After Humanity" era where Pokemon have become capable of intelligent speech.
Humans have permanently departed from the planet in a massive Space Exodus, leaving behind their infrastructure as the only evidence of their former presence.
Humans still exist in the world but the location that the story of Red/Blue Rescue Team takes place is largely unknown and inaccessible to them. The Decrepit Lab is possibly evidence to a failed attempt at colonization or just a remote research station that met with disaster.
Since Mewtwo was created by humans, he might be the only Pokemon in the series who has some knowledge and history about them. But it remains an unexplored plot hole since no one bothers to ask and he never says anything about it.
Unlike the main Pokémon series, "movement speed" actually provides a Haste effect, giving the user multiple turns in a row. It wears off quickly, but a quickened Pokémon can inflict a lot of damage if they also know attacks capable of hitting an entire room. This goes double in Monster Houses, where an enemy Pokémon using "Agility" can increase all enemies to double/triple/quadruple turns.
Due to the lack of genders in the original games, Attract could effectively disable anything in Red and Blue for several turns, even bosses.
Multi-Hit attacks (Bullet Seed, Fury Swipes/Attack, Pin Missile). Due to the damage calculation in the Mystery Dungeon games being much different than the mainstream titles, these moves now hit as hard as most other attacks each individual hit. This is made worse for the fact that the STAB bonus from the mainstream titles is also implemented in the Mystery Dungeon games, meaning with the right Pokémon (A Treecko with Bullet Seed and the Concentrator skill for instance), this can be quite lethal.
Petrify or Foe-Seal Orbs render Monster Houses pretty much trivial: they freeze every enemy in the room until attacked, letting you mop them up one by one and gather the sweet loot. What's more, your A.I. team is smart enough not to attack any enemy under the effect, so you don't have to worry about them ruining it and dooming you.
Goddamned Bats: Pretty much anything that can inflict Poison status, attack from a distance (most Water-type attacks have ranged capability), or from within walls (the Ghost types).
Doom Seeds: You better pray that an enemy 'mon doesn't throw these at you...
Spinarak, a mon that can cause the aforementioned poison along with a slow, causing it to go twice as much as you.
Magnum Opus: The Explorers games for their story, which is considered one of the best in Nintendo history.
Nintendo Hard: Especially the bonus dungeons, some of which totally empty your inventory and level you down to 1. It's because of this that Purity Forest and Zero Isle South are many players' favorite dungeons.
Stop Helping Me!: AI teammates often embrace this trope with both hands, especially with low IQ stats. Reviving an entire room of petrified enemies with an ill-timed Growl attack, for example.
Magnagate has also been hit with this since the Japanese demo was first released. For details, see its entry below.
Tier-Induced Scrappy: Pretty much anyEscort Mission you do will include this. You can't assign tactics to them if they get separated, and in Red/Blue Rescue Team the escorted Pokémon was almost always at Level 1, making it easy for enemy Pokémon to KO them. To put it nicely, these are the guys who tend to waste all your Heal Seeds and Reviver Seeds for doing annoyingly stupid things like wandering off and walking into lava/fire. Explorers was just a little bit nicer in the levels department, but your clients are still under-leveled.
Tough Act to Follow: Gates to Infinity is having a very hard time following the Explorers games, mostly for "not having a deep enough plot", and the fact that there is a lot less post-credits content compared to the other two games.