In Joe's streams of Undertale, he named the protagonist "Waffles" for no apparent reason (except it was actually "Waffls" because of the character limit).[1] Since then, it became a tradition in every game for him to name the protagonist "Waffles".

“All the Waffleses in a waffle bar” by Mr. Sunrise, featuring: Waffls, Waffles Dadapon, Waffles Chadapon, Waffles Cardapon, Waiffles Buzzellapon, Waffles $adapon, Waffles Wizzapon.
"I don't really even like waffles."
—Joseph Anderson

If he ever doesn't call the protagonist Waffles or some variant of it, he sometimes calls them "Joe the hoe" instead.

Dadapon

Joe named the protagonist of Persona 5 "Waffles Dadapon".[2] He also did a voice for this character. Dadapon is represented by the emote  jphWaff.

Waiffles

In Genshin Impact, Joe named the protagonist "Waiffles", which is a portmanteau of "waffles" and "waifu".

Chadapon

In Persona 4 Golden, Joe named the protagonist "Waffles Chadapon". Chadapon is represented by the emotes  jphChad,  jphChadroll, and  jphDreamcome.

Cardapon

In Inscryption, Joe named his first Deathcard "Waffles Cardapon".[3]

Buzzapon/Buzzellapon

In Starfield, Joe named his character "Waffles Buzzapon", in honor of Buzz Aldrin.[4] During his playthrough Joe encountered a bug that stopped his character from firing weapons, which could only be fixed by changing his character's gender. When he did this he renamed her "Waiffles Buzzellapon".[5]

$adapon

In Persona 3 Reload, Joe named the protagonist "Waffles $adapon". $adapon is represented by the emotes  jphSada and  jphNoparktoday.

Wizzapon

In Baldur's Gate 3, Joe picked the wizard class and named his character Waffles Wizzapon.

References
  1.     “Joseph Anderson Channel Two” video: “Undertale First Blind Full Playthrough” at 00:10:15.
  2.     “Joseph Anderson Channel Two” video: “Persona 5 - The Pure Positivity Stream (Stream One)” at 00:22:15.
  3.     “Joseph Anderson Channel Two” video: “The Card Game Escape Room (Inscryption - Part One)” at 01:58:20.
  4.     “Joseph Anderson Channel Two” video: “The Naked Astronaut (Starfield - Part One)” at 00:57:35.
  5.     “Joseph Anderson Channel Two” video: “The Game Breaks And I Can't Shoot Any Guns Anymore, Unless... (Starfield - Part Five)” at 01:02:44.