Before we get anything else out of the way, I know what you're probably here for. Final PC body count:
Maes Hughes: Killed by Diego's Razor Floss, which was then used to string him from the mast of the Way. This death was later retconned, but its status (as the Dead Serious marker, being the first PC death), the effects it had already had on the plot, and the fact that he didn't do much after being re-apped by a different mun until he was dropped again make the retcon dubiously canonical.
Kristoph Gavin: Sentenced to death for something he actually didn't do, taking the fall for vK. His fate was left ambiguous in case somebody else apped him, but was finally confirmed by Word of God after the game was over.
Sam Linnfer/Lucifer: Not dead, but lost his mind as a result of a Dangerous Forbidden Technique, making the Sam we know and love only one easily-silenced voice among many. Word of God is that he'll never recover.
Optimus Prime: Defeated holding off King Bradley, left for dead. Died onscreen (as it were) when members of his crew came back to get him.
King Bradley: Fought to the death with Hollow Ichigo.
Dinobot: Fought to the death with Hollow Ichigo.
Kiryuu Kaoru: Defeated and left for dead by Void. Later recovered, only to die in an infirmary bed in the Playable Epilogue. Because of copious unintended foreshadowing before she died, she now haunts Serenity.
Dueling Games: Marshmallow Mateys was, early on, compared to TST because they had player-run ships instead of mod-run... even though the games were nothing alike (one was a plot-heavy steampunk adventure AU and one was a jamjar based on One Piece). After TST proved that mod-run ships were much better for what it was trying to do (and the other game died a slow death), this diminished.