"Half Pain" from Witch Hunter Robin.
"Down the Distant Road" from Inuyasha the Final Act. Pretty much all Inuyasha endings though, to be honest.
"Gravity" from Wolf's Rain.
"Shiki no Uta" from Samurai Champloo is one of my ALL TIME favorites. But I liked when they switched it up with "You" and "Who's Theme," too. All of the music in that anime was just incredible. Leave it to Shinichirō Watanabe, though, seriously. That guy is a master. Which brings me to "Real Folk Blues" from Cowboy Bebop, most def.
The ending theme for Please Save my Earth is super gorgeous.
"Motherland" from Fullmetal Alchemist (the trash anime, aka not Brotherhood, lol), is definitely one of my favorites, too. c: Kind of an unpopular opinion with that one, but I remember it really touched me when I was little, pfffpht---a girl and her dog. It hit home.