My favorite game ending is one of the most polarizing endings in the history of video games, Metal Gear Solid 2. (sorry, this may be long)
The game's message about the flow and control of information in the age of the Internet was way ahead of it's time. In 2001, it may have just seemed like an exaggerated commentary on message boards and blogs, but since then, we've seen media blackouts in many countries where twitter is the only way to get information out, the FCC Net Neutrality ruling, partisan 24-hour news networks manipulating facts and using editing tricks to express a political view point which is then presented as"news," and events like the Wikileaks scandal. When one considers the current state of the media and information control, MGS2's ending becomes very relevant.
As far as the actual story goes, you are just waiting to fight Ocelot the entire game, which never happens, and it leaves you waiting in anticipation for a confrontation in the next game. It was a beautiful build-up to the final fight in MGS4 (regardless of how you felt about the pay-off, the build-up was nice, at least).
Jack is struggling with ideas of choice, which seems to be a major aspect of Japanese story-telling, "Why am I fighting?" and it leaves the player questioning his or her own actions. By the end, you realize that Solodus is kind of the good guy, so, when you are forced to kill him, you feel bad about it.
The lighting, blocking, and music in the final cut-scenes, are all executed perfectly.
When Emma's GW virus starts to kick in, the game breaks the fourth wall and starts messing with the player in a very "Eternal Darkness" kind of way. The "Fission Mailed" screen is very meta. It presents an interesting message. Like Jack, you think you are in control of your actions while playing the game, but actually, the game's system is, not the player. You have the illusion of control through most of the game. It all feels standard and routine, until the GW virus goes into effect. The last few hours of MGS2 are about what happens when the illusion of control starts to break down, for Jack and for the player. "Fission Mailed" plays in because part of the message is that if the game's system is designed to kill you at a certain point, it will, regardless of what you do. You think you are in control, but to what extent? In an admittedly insane conspiracy theory kind of way, it's designed to make the player consider how much control they really have over their own life. I think it's similar to the message presented in The Matrix.
It's a challenging ending, but one you can take something different away from every time you play it. It's definitely post-modern and is designed to make the payer reflect on many hidden themes. It's an ending you either get or you don't. It wasn't made for everyone, and that's ok. This is why I wouldn't call it the "best" game ending, but it certainly is my favorite. To quote Wayne's World, "Led Zeppelin didn't write tunes everybody liked. They left that to the Bee Gees." That's how I think of Hideo Kojima. In that sense, he's the Led Zeppelin of game development.