I liked the intro sequence of Snatcher (Sega CD) a lot. Especially the part with the cool 80s style electro beat with lead saxophone. That was the moment I fell in love with it
My favourite ending was the Vagrant Story credits. Again, the music kicked butt hard! I'm a big fan of Sakimoto's compositions, but that time he really blew me away by actually making a full orchestra play a reprise of the most memorable themes in the game.
The second best ending was the one in Terranigma, again for its wonderfully sad music and theme.