I did one of these a while back, but a lot of things about my fanfic have changed since then. I hadn't even started writing it at the time I made the original list... So here is the new and improved list of TV Tropes that apply to my Pokémon Mystery Dungeon 2 fanfic! This is mainly for my own amusement, so feel free to ignore this if you do not know of / like TV Tropes.

Main Tropes:
Action Girl - Pretty much any named female character, though it's more evident for some than others.
And I Must Scream - Happens to Ditto.
Anything That Moves - Iris. It's especially noticeable in the Team Rainbow crossover, where she tries to claim Ricky even after he gives up and accidentally knocks himself out.
Back Story - The first two chapters.
Battle Boomerang - Rin's favored method of attack is Bonemerang.
Beware The Nice Ones / Beware The Quiet Ones - Rin can get this way when dealing with Iris.
Butt Monkey - Bruce. Iris identifies him via Offhand Backhand, Team Shadow is taken to the future right after he joins, he gets left behind, and, in the crossover, he gets shocked repeatedly by Paula's cousins.
Cool Big Sis - How Felix views Claire.
Deadpan Snarker - Mainly Sydney and Maryn, though Iris gets a few good snarks in too.
Ear Notch - Claire has one.
Elemental Punch - Iris is very fond of them.
Genki Girl - Heliona and Claire, and especially Heliona. Celebi and Mesprit are more minor examples.
Get Ahold Of Yourself, Man! - Iris does this to Felix in chapter 9.
Good Scars, Evil Scars - Claire plays with the trope in that she has scars, and she's definitely good, but the scars are the huge kind you'd expect to see on an evil character.
Hot Blooded - Iris, very much.
Interspecies Romance - Michelle and Blitz.
Kick The Dog - Chatot tries to use Claire's amnesia against her when Team Shadow gets back from the future.
The Mole - Missy.
Motor Mouth - Heliona can be this way at times. It's highlighted in one of the side-chapters, where Chatot tells her to slow down.
Nice Guy / Nice Girl - Bruce, Claire, and Kerry.
No Sense Of Direction - Heliona, much to Sydney's exasperation.
Noodle Incident - In one of the side chapters, Iris mentions that she never wants to go near a Skuntank again (right before meeting Team Skull's leader). Rin assures Claire that she does not want to know what happened.
Offhand Backhand - Another thing Iris is fond of.
The Quiet One - Rin and Andrew.
Shock And Awe - Claire and Andrew are very fond of Thunderbolt. They learned it from Blitz, so he counts, too.
Shrinking Violet - Leon and Felix to varying degrees.
Sugar and Ice Personality - Leaf/Grovyle, as well as Andrew to a lesser degree.
Team Mom - Kerry of Team Aura Blade has hints of this.
Tsundere - Skorupi is tsundere for Leaf/Grovyle.
Unstoppable Rage / No-Holds-Barred Beatdown - Leaf/Grovyle towards Ditto after Ditto transforms into Claire.
"Well Done, Son" Guy - Felix has shades of this, as revealed in chapter 11. Though he also admits that his parents care about him more than is usual for this trope.
With Friends Like These - Rin and Iris are polar opposites, Rin frequently gets annoyed with Iris, and Iris sometimes comments that Rin is too serious... and yet, they're best friends.

Your Mileage May Vary Tropes:
Fan Wank / Epileptic Trees - Several deliberate, in-universe examples, mainly happening during the first two chapters, such as theorizing on how the hero met Grovyle and filling in some specifics about the Dimensional Scream ability.

Trivia Tropes:
Development Hell / Saved From Development Hell - This fic was in various stages of planning for years before getting posted.
Name's The Same - Grovyle has the same nickname as the Fire Red / Leaf Green heroine.
Shout Out - One to Princess and the Frog in chapter 7. Heliona claims she got distracted by "the geography, topography, and choreography." Sydney then claims that there's an unofficial rule of the guild to never take directions from a Vulpix. This is quite similar to some of Louis and Ray's dialogue.
Then, chapter 9 is titled "Back To The Future".
Tribute To Fido - Jack and Blitz are named after ~Latias-Eevee's dog and old cat, respectively.
What Could Have Been - The current story varies a bit from what was originally planned. Some of the more notable examples include Claire having an older sister (who was a Cat Girl with more Meowth traits) instead of a twin brother, and several characters (such as Missy, Bruce, and Teams Lightning and Aura Blade) either having much smaller roles or not being included at all.

Fridge Tropes:
Fridge Brilliance - The one time Iris is specifically mentioned to use Thunder Punch is during the Get Ahold Of Yourself, Man! scene in Chapter 9. Since Claire's favorite move is Thunderbolt, Iris's use of Thunder Punch here is meant to emphasize that Felix needs to listen to Claire's directions.