Gee, it's a tough one. It's a great album, without a single bad track. The closest you get to 'bad' is The Mercenary which is just a good song, but nothing spectacular.
After considering all the options, it all comes down to three tracks. Ghost of the Navigator, The Nomad and Dream of Mirrors. The Nomad is, just as Alexander the Great fantastic in terms of music. But just like 'Alexander' it lacks in the lyrics.
So now, there's only two left. Dream of Mirrors is a fantastic song. Though it takes too much time for the song, to really 'get going' it's still one of my favourites. The lyrics are spectacular and just... Twisted. "I only dream in black and white. I only dream 'cause I'm alive". It's like taking a trip into Steve's mind.
And finally. Ghost of the Navigator. Though it's better live, it's still a great song on the album as well. Thinking of the broad perspective, the songs are just equal. But, to determinate my favourite, I'll just have to go with the song which have the best chorus. There's really no other way. And the winner is: Dream of Mirrors, because of its fantastic chorus with the heavy riffs.