I think the most overused one is the classic 'Loyalty Test' twist, where Hermione discovers her lineage early, but Voldemort orchestrates a scenario to prove she'll choose him over the Light. It usually involves forcing her to torture a friend or reveal Order secrets. The predictable part is she always fails the test or turns it back on him, proving 'love conquers all.' Seen it a dozen times; it gets stale because it ignores Hermione's core trait—her intellect—and reduces her to a pawn in a very obvious game.
A more interesting variant I stumbled on had the twist occur after the final battle. Hermione, now a respected Ministry figure, starts having uncontrollable bouts of Parseltongue and nightmare visions linking her to Nagini's consciousness. The real twist wasn't the parentage itself, but that her magical core was fundamentally Dark, a fact suppressed by Dumbledore's charms on her as a baby. Her entire academic prowess became a tragic irony; she was studying a magic inherently opposed to her nature. That created a much messier, more compelling internal conflict than another 'chosen one' narrative.
Honestly, the parentage reveal itself is rarely the actual twist. It's the catalyst. The real plot twists are in the consequences: Ron's betrayal feeling justified, Harry's isolation becoming absolute, or Hermione realizing Dumbledore knew all along and manipulated her path. The fics that linger with me are the ones where the twist isn't about shock value, but about dismantling her identity so completely that even the reader isn't sure who she is anymore.