Hmm, tough one....
One that INSTANTLY stands out for me is Pink Floyd's Shine on you Crazy Diamond Parts 1-7 (especially on the best of release, which I have, and the whole song is pieced together.) Man I love this track.
Another is again, Pink Floyd's Echoes. VERY moving, atmospheric song and it's just flat-out excellent.
Opeth's Black Rose Immortal, yes, SHOULD be metioned here. It's the song that got me into Opeth in the first place (the clean passages in particular at the time blew me away more than anything else I have heard at the time.)
9-29-045 from Green Carnation's EXCELLENT Acoustic Versus - turns out that this song happens to be one of my favourite song of the year so far. So many fine moments here - insanely well put pieced together.
The Everlasting from Virgin Black's Elegant...and Dying album - simply magnificent! 20 min of pure splendour and amazing build-up. Highly depressive and emotive music you'll only enjoy listening to alone. Something you can't really sit down and enjoy with a buddy or two, hehe.
Hmm, I think that's all that comes to mind right now. I'm trying to think of others, but VERY large songs are quite rare. Oh, and light of day, day of darkness didn't really ever do anything for me. I wish they were broken up into parts because listening to one entire song like that just isn't my thing.
Ah yes, I MUST included my favourite classical composer Frederic CHOPIN - any of those outrageously lengthy nocturnes he has or any other piece he has ever created is a musical orgasm. Seriously, listening to his music is greater than anything else - it soothes the soul. It's like i'm at my own peace and nothing else really matters - it's just me and the music taking me away.