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6:00, from Awake, is based on a short story called "the Dead" by an Irish writer called James Joyce. There was a film made of it too, and thats where all the "for the honour of god " quotes came from.

I read the story on the internet when i found out. It's strange, because you feel all the way through that something really bad is going to happen, It's got a really scary atmosphere, but it's more of a story to make you think than actually scare you. It sort of fades out at the end, and nothing that really stands out happens in the story, so you really have to read it to see what i mean.

I'm just looking through my CD collection now and seeing what I remember.

A Fortune In Lies - this was something to do with one of Mike Portnoy's friends who once got them all into trouble.
Status Seeker - I submitted a lyrical analysis to DTFAQ about this one, but it never got put up, and I forgot to save it because I'm doofy. D: I basically came to the conclusion that it was about the band's struggle finding a label and getting everything together etc.
Ytse Jam - Basically James LaBrie's biography.
The Killing Hand - John Petrucci basically thought "hay, i like the twilight zone, let's twilight zone up the joint!" and made a story based on that kind of thing. D:
Light Fuse and Get Away - This one's basically about meaningless sex and cheating on people. From what I gather, someone on the WDADRU DVD (MP probably) said that the title basically translates to ******** and flee.
Don't know any of the rest from WDADU.

Pull Me Under - Deals with coping with the loss of a friend, some passages loosely based on Shakespeare's "Hamlet."
Another Day - Something about John Petrucci's father's struggle with cancer, or something to the effect.
Take The Time, Surrounded - God only knows.
Metropolis Pt. 1 - John Petrucci's attempt at a roman myth. :D
Under A Glass Moon - PLEASE, SOMEONE, TELL ME. Most senseless song evar.
Wait for Sleep - From what I gather, it's written about a friend of KM's who was grieving or suffering from insomnia or something like that.
Learning To Live - About struggling through the AIDS epidemic.

6:00 - I think that in addition to whatever the cool guy above me said, this was basically Kevin Moore's mixed thoughts about leaving the band.
Don't know, don't know, don't know, la la la la la. I'll just leave out any I don't know from now on.
The Mirror - Think of it as a prequel to The Glass Prison. :D Subject of alcoholism, but before going to AA or anything.
Lie - Seems to be about an unstable relationship. "So you tell me "trust me," I can trust you as far as I can throw you," "She comes in apparently to fill the void" seem to suggest so.
Space-Dye Vest - Similar to Lie.

Peruvian Skies - Based on an article that touched John. About a girl who was abused (in Peru).
Hollow Years - I've got a feeling this is either about cherishing either life or a relationship.
Burning My Soul - As I Am part 1. :P Basically "quit telling us what to do," aimed at the label more than anything.
Just Let Me Breathe - A tongue-in-cheek attack on the music industry.
Raise The Knife - I think this one deals with the mixed feelings and tension between Kevin and Mike.

Scenes from a Memory - I can't be bothered to go into depth.

The Glass Prison - as said above.
Blind Faith - About religious zealotry, and kind of saying "look, there's more than one way to look at things. you're not always right."
Misunderstood - Eee, I forgot. Something about Jesus. D:
The Great Debate - Presents both sides of the debate regarding stem cell research.
Disappear - I'm not certain. I believe it has something to do with the death of James LaBrie's mother, however.
Six Degrees of Inner Turbulence - I posted an analysis on dtfaq.com (I'm R Webster :P), so check it out! In short, it focuses on six people with different psychological problems and difficulties.

As I Am - "yaaaaar, i'm john petrucci, and i like doing what i like doing."
This Dying Soul - The Glass Prison part 2.
Endless Sacrifice - Separation from his wife while on tour.
Honor Thy Father - "yaaaaar, i'm mike portnoy, and my stepfather is made of poo."
Vacant - Whoever said it was about JLB's daughter was probably right. I like the idea.
Stream of Consciousness - A moving account of James LaBrie's adventures in walmart. That little rap bit in the middle is his shopping list.
In The Name Of God - More religious zealotry, this one more about how religion can twist people and how repulsive extremism is.

The Root Of All Evil - Glass Prison 3. As a side note, "Root" in its title is because F is the root of the octave, and that's the theme thingy throughout octavarium. :D
The Answer Lies Within - I think John wrote this to his children or something. From what I remember, at any rate.
These Walls - Feeling muted and absence of communication.
Panic Attack - I think this is about a midlife crisis. Not sure at all, though.
Never Enough - We all know this one. :D
Sacrificed Sons - "yaaaaar, i'm james labrie, and i don't like terrorists." Based on the attacks of September 11th.
Someone Like Him - I think this is about anyone really (I don't think it's John Petrucci reflecting on himself), and how all the time he's pursued great things etc., but in the end, he just wants to be himself day by day - just like his father was. Basically, someone who's aimed so high and had such a hectic life, and now that he's there he realises that he's missed out on so much of the normal day by day stuff. Comes into the theme of "a life I never had" that runs through the mellow section of Octavarium.
Medicate - Based loosely on a Robin Williams film called "Awakenings." (great film :D) Again, a theme of "a life I never had," but this person never had the opportunity - the protagonist has been in a coma for thirty years.
Full Circle - Tribute to influences and etc. Anyone who wants a rundown of all of them just go to a concert, they flash them all on the screens when they play it. (I still haven't got over how awesome that concert was. D: ) Though Day Tripper, Supper's Ready, Gabba Gabba Hey etc. are all references to influences, they have some stuff in there like Owen Wilson, Jack The Ripper, Nightmare Cinema and the likes that are to do with miscellaneous stuff.
Intervals - Track by track analysis of the album. Every four bars (I think?) refers to a different song. "Our deadly sins feel his mortal wrath, remove all enemies from our path..." is The Root, all up to "Step after step we try controlling our fate, when we finally start living it's become too late" for Someone Like Him/Medicate.
Razor's Edge - I got nothing. Just a Rush reference in "a perfect sphere," and the fact that it works as a finale. I don't know what the first stanza is meant to mean ("we move in...razor's edge").

Vacant was written about James LaBrie's daughter going through a seizure of some sort. If you want to listen to more about what he says, go to the JLB interview on delicious agony radio: click here to download it. It's a really good interview.

A good site for song meanings is the DT FAQ. They don't have everything, but they have a large database.

Any song you want to know the meaning to, go here. This site has pretty much everything, even with DT. 3nodding

In my opinion, when looking at the lyrics of a song I think the point is to take the meanings you want from them. Whatever they mean to you, however they make you feel, that's what the song means. It doesn't have to be the same for everyone.

I completely agree with both of these statements. I've looked at a lot of songs and gotten totally different meanings from them at different times, or meanings totally unrelated to what the songwriter intended.

I read some book in seventh grade that said something about how a story has something different to give to everyone. That sort of reminds me of this situation.