I think a perfect ending has a sense of meloncholy. Things shouldn't all wrap up perfectly, it just makes it unsatisfying. I also enjoy ending that leave you wanting more without just smurfing with you and throwing in something just to make you play the next game. Spoilers ahead.

Final Fantasy VIII - I agree is a great ending. I like when Seifer looks up at Balamb garden and has a feeling of regret, and the end where it looks like Squall dies, and then you see him and he smiles for the first time, very satisfying

Final Fantasy VII - We all know now but that ending was great because you really didn't know if any of the humans survived it, were they good for the planet or not? I also love the last line where I think Barret asks what the hell those green swirling things are and I love the way Cloud responds, "Lifestream," and then it shows everyone real quick and a last shot of Aeris from the opening.

Suikoden - It is perfectly bittersweet because you feel bad in a way for taking down the empire, and Mathiu dies in a great scene, and you don't know the fate of Viktor and Flik. I also love the scene where it says what happens to the stars of destiny. I think the first Suikoden did the best in making the most of those stars memorable characters, at least 70 of them you feel something for.

Suikoden 2 - Same as the first one, as you begin to realize the Jowston and Highland armies are fighting for the exact same thing, and either your character or Jowy would be equally great and fair ruler, it's just one has to be on top. Also the three endings with Jowy and Nanami are all bittersweet, particularly the one where after the credits is just shows a picture of Jowy waiting at the rock where you and your character promised to meet one day.

Final Fantasy Tactics - Great ending, where Ramza and Alma, have to disappear into secrecy, and are branded as heretics, and Delita stabs Ovelia (although I don't think kills, he stabbed her so he could fake her death and let her live in freedom), it's just a perfect example of what an ending should be, lot's of emotions good and bad you feel after it's over. Delita asking "Ramza what did you get, I...." makes you think.

Vagrant Story - Same as Tactics, so many emotions in it. With Ashley coming to terms with his past, and guildenstern dieing, and tieger fighting with grissom("tis a fine tomb we shall share") and Hardin, Josh, and Merlose escaping as well as Ashley carrying Sydney. The death scene with Hardin is as good as it gets, very simple in a perfect way. Then the scene where the duke and sydney die is great, and the best last line in any game,
"And so began the story of the wanderer........The Vagrant."