ICO <object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/82ugj5m9BCs&hl=en&fs=1"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/82ugj5m9BCs&hl=en&fs=1" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="344"></embed></object>
I always thought the Contra ending was awesome. Also the first Metal Gear Solid I thought was very awesome for its time.
I was gonna mention this one and Shadow of the Colossus. Easily two of my favorite games ever, and both of them nearly brought me to tears. I've never experienced a game like these two.
<object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/7jb4Ws1lPHc&hl=en&fs=1"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/7jb4Ws1lPHc&hl=en&fs=1" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="344"></embed></object> I don't know about best ending, but it was the saddest ending to a game I've seen. Poor Zack...