The End of Evangelion was everything an ending should've been.
The Melancholy of Haruhi Suzumiya had its episodes out of chronological order, so while 14 was--timeline wise--episode 6, it was an amazing ending.
Berserk was sick and mindblowing, but just barely the beginning for the manga.
As far as the best ending I've ever seen, Giant Robo takes that spot.
Honorable mention goes to Dragonball Z just for the fact that it ended.