Ghost Reveries is possibly a top 10 all time album for me (or very close) so I obviously adore everything about it. The Baying of the Hounds is not often a song that springs to my mind as a favourite, but it is awesome.
As with every song on the album, it's filled with twists and turns, contrasts from heavy to light and changes in pace. I think of all Opeth's albums I love Ghost Reveries the most because of their mastery of these contrasts.
As for favourite bits, the "Everything you believed is a lie" part, as well as the solo just before the 7 minute mark. Yea, just an incredible song.