The Godslayer, The Final Instance or The Last Remnant all from The Last Remnant. The require, in order, beating the ultimate optional boss (2 million hp I believe, `10 rounds or less. After round 10, he auto game overs you. He has attacks that hit the entire battlefield at once. Good luck.), beating every quest in the game (Quite a few are Guide Dang It's that you'll very easily miss.) and beating the ultimate form of the game's final boss. The Atlus developer's blog says they make their games hard because they get off on player's tears. Someone at Square-Enix took umbrage with that and decided to outdo them, because the TLR final boss is one of the hardest in his -normal- form, much less ultimate form.
Honorable mention goes to Armored Core: For Answer, which has an achievement that requires getting 10,000 wins online. Yeah, that's not a typo. 10,000. Online. Wins.