FFVII's ending gets me every time, and I find it undiluted by the sequels. In my mind, the '500 years later' sequence was never meant to imply that (SPOILER)humanity had perished. Rather, I find it somehow heartwarming and bittersweet. Half a millennium's passed; Cloud and the others are all long since gone, yet Nanaki's still passing on to his children the tale of his long-dead friends and how they gave their all so that the world could live. The heroes get remembered for what they achieved, and that's just swell to me.

MGS3 is another worthy ending. (SPOILER)Naked Snake/Big Boss gets used, abused and basically shat on by the principles he's been fighting so hard to protect - it makes it understandable just why and how he'd go on to become an enemy to most of the world.

MGS4 ended on an odd mixture of catharsis, over-the-top revelations and truly rampant tying-up of loose ends. I'd probably lump it somewhere in the 'WTF' category.