I remember first starting out in WoW, back in Vanilla, Only went to lvl 60 times, everything had been pretty much standard fantasy fare for starting out as a Night Elf. Then in Darkshore, I came over a rise and came face to eyehole with a massive, alien skull. That's burned in there pretty good.
Best sequence ever though? Okami. The Final Battle. The cutscene with "ReSet ~ Thank you Version ~" and then into "The Sun Rises" as you unleash an industrial sized can of whoop-ass. I was crying Manly Tears through that whole battle.