1. Chrono Trigger #12a-"OFFICIAL ENDING"
Crono's stay of execution is cancelled, he's a hero, blah, blah...they go to the fair, everybody goes home, then Crono's mom chases all the cats (they're running away, because "Crono didn't feed them", regardless of how much Cat Food you have), and the cats and Crono's mom go in the gate, and you go in Epoch and try to find her.

2. Chrono Trigger #1-THE DREAM TEAM
This ending is great. You'll end up in the End of Time, and you can go around and talk to all the programmers who made this game. Once you've talked to everybody, go to Spekkio's room.

3. Chrono Trigger #8-REPTITES!!!
Starts just like the beginning of the game, but all the humans are replaced with Reptites!

I loved Bioshock as a game, but honestly thought that the endings were a little on the weak side.  They just felt very...abrupt, almost like they were put in as an afterthought.

IMO the best game ending I have played in recent memory was Mass Effect.  The last two hours were simply epic as anyone who has played the game will no-doubt agree.  It will be very interesting to see how the beginning of Mass Effect 2 accounts for your end-game decisions in the first one.

I can't really remember an ending that stood out as great. The worst endings for me would be.

1)GTA4
2)HL2 EP2
3)Bioshock

1) MGS1
2) MGS2
3) MGS3

LOL, they are all just so great, I will be beating MGS4 this week

Every MGS game ending after the credits.

1. Majora's Mask

2. Okami

3. Mike Tyson's Punch out!

I could think of better ones, but those were the first 3 that came to me.

1)gta4
2)mgs2
3)Final fantasy VII

Space Channel 5
Shenmue 2
Elite Beat Agents

Runners up : Sonic 3 & Knuckles, Contra III: The Alien Wars/Super Probotector: Alien Rebels, Super Metroid, Quackshot Starring Donald Duck

- Final Fantasy VII (barely remember it because it's been so long sinse I've played it but I know I was amazed when I watch the end)

- Portal (from The Orange Box, lol I love the ending song)

- and probably the best ending you could make for a video game was on God of War 2 (I can't wait for 3!!!)

Severe lack of Shadow of the Colossus in this thread. As for two others, I guess HL2 and Suikoden II (really need to buy a copy before they get even more expensive).