Very good and underrated year to kickstart the new millenium! Obviosuly the Dreamcast had an outstanding year with the likes of Grandia II, Phantasy Star Online, RE: Code Veronica and ofc the wonderful Skies of Arcadia. N64 was winding down but Majora's Mask is a top Zelda game imo. The PS1 had its last hurrah this year with Vagrant Story, Dragon Quest VII, and my vote for GotY 2000, Final Fantasy IX.
Skies of Arcadia ran it really close for me, but while Skies had better combat and exploration, FF9 had a better story and characters and that's more important to me personally. Both had exceptional soundtracks too!