Before the Demise, which is actually the final boss theme. It's most unlike final boss themes, which are often trying to pump you up.
The DS version's opening theme, Follow the Nightingale. Also doubles as the music for Mathias's final form in Innocence R.
Demonic Spiders: After the events at the Sky Castle, Luca is dumped into the desert, separated from the rest of the party, and has to make his way to a nearby town. Some of the enemies can petrify on attacks, and if your entire party is petrified, game over. Your entire one character party. And if you didn't save before attempting to cross the desert, you get to sit through a long cutscene again, too. Luckily, the town is very close by, so it's quite possible to bypass battles.
Ensemble Dark Horse: Spada, at least in the Japanese fandom. He is the only character from Innocence to appear in the top 30 of Namco's popularity polls, not to mention appearing twice, in the 4th and 5th polls.
Ho Yay: Due to the nature of Relationship Values, players can pair Luca with whoever they want (at least, in the original version). There are some notable ones story-wise, though, especially in R.
In the original, when Luca recovers after he was stabbed by Hasta, Spada hugs him◊ twice (and attempted the third). In R? It goes way back to early in the story not long after they meet, where upon finding out that Luca is the reincarnation of Asura, Spada immediately hugs him while telling him that he (as Durandal) missed Luca/Asura...before it is humorously cut short by Iria. Luca's reaction does not help matters. In R, they are upgraded to Bash Brothers, with some of their victory poses have them cross their swords in the air together.
Kongwai/Luca. In the Relationship Values screen, Kongwai notes Luca to be "interesting", among other things. He is also one of a few who actually treats Luca well.
For some Les Yay in R, Hermana's obsession with Ange's assets now manages to give Spada's a run for his money.
The past life side has Himmel and Orifiel, who mean so much for each other that Albert/Himmel intended to sacrifice Ange/Orifiel to activate the Manifest.
Older Than They Think: Much of the game's premise is eerily similar to the backstory of White Wolf's Exalted RPG, down to the past-life superpowers and conspiracy about the downfall of the main character's previous incarnation.
Player Punch: In the Tower of Dawn, Luca and Co. are confronted by Oswald piloting the new-and-improved Gigantess Omega and reveals, too much to Ricardo's horror, that is powered by Gardel/Thanatos' corpse. Ricardo swears that Oswald will pay for desecrating the remains of his brother. The party, too, is more than ready to rip Pigwald a new one.
Viewer Gender Confusion: Himmel. His hair is caught in a long, flowing, braid, his outfit is very androgynous and his face is probably more feminine than anyone else's. His voice doesn't help.
YMMV tropes applicable to original version:
Woolseyism: The fan-translation takes this path for a good fraction of the game, which is noticeable if you listen and cross-check the voice-acting and translated scripts. They don't translate word-for-word, and instead focus on fluency. The very first example is replacing "Tenjo" and "Chijo" with "Devaloka" and "Naraka", which is Sanskrit for "Realm of the Devas"/"Heaven" and "Hell" respectively. It makes sense in context of later revelations, as the game draws a fair amount from Buddhism and Hinduism. And you know, if literalism is your thing, you actually have the option of turning off the Woolseyisms...for terminology, anyway.