I'll add a few that haven't been mentioned (I think):
Agalloch - In The Shadow Of Our Pale Companion
Just a beautiful song all around, that builds and builds, and then just breaks in your face - all the while the band manage to refrain from going crazy and since they hold back, it gives the feeling of an almost 'delicate' track.
In The Woods - 299.796 KM/S
Took me some time, but I love this song. The unique singing style (along with the female singing) is great, and I love how the song takes it down a notch during the middle and then comes back up again.
Green Carnation - Light Of Day, Day Of Darkness
This song has it all - great riffs, great singing, everything. If it wasn't for that chick singing a couple of minutes too long, it would have been perfect. Also, the solo for this song is one of my favorites - not techincal at all, with a lot of feel.
Subterranean Masquerade - Temporary Psychotic State (a recollection of where it all began)
I couldn't decide which track of theirs to choose, and in the end I went with the EP track. It took me a while to completely grasp this song, and once I did, it was just... wow. Paul Kuhr really gives his finest performance with great lyrics.
Symphony X - Rediscovery II (The New Mythology)
Mainly for nostalgic reasons - one of my earliest metal experiences. I still think it's a great song, despite the fact that it's wankery or whatever, it just has it all - awesome singing, great heavy riffs, nice idea too.