You may be thinking of another game. In Arkham Asylum, they disabled the glide function ([1]), you definitely knew about that before the final boss.

Now, EarthBound had a hook like that one [2], where the game would first make it much more annoying to get through the game (by churning out extra random encounters), and then when you get partway through the final boss the game will freeze and delete your save game.

[1] http://forums.eidosgames.com/showthread.php?t=95030

[2] http://earthboundcentral.com/2011/05/earthbounds-copy-protec...