Nemo

Straight from the songwriter's own mouth:

"Not the fish! I cannot believe how everyone seems to be convinced it’s that. Nemo, which is Latin for "nobody," has nothing to do with the Disney film. It revolves around the feelings I have from time to time. I feel nameless and do not know who I am or where I will go. I only know my past and I long to be back there. The song is about being lost, not knowing where to go or what to do, yet desperate for everything in life. That’s not always me, but when I wrote Nemo, that’s the way I felt. Now I feel better." (Translated from the German)

–Tuomas Holopainen, Underground Empire interview

the Nemo=Nobody fact is correct and that's waht Nemo means in this song

the song is about being nothing (atleast feeling as you're nothing) or not knowing who you are, if you've seen the video, then you see that she disappears into thin air at the end of it...

Mordred is right, Toumas is the mastermind behind Nightwish, tarja is the voice sent from heaven to spread his message.

Nemo is all about feeling missunderstood and having no identity, no place in this world. It is the endless struggle to find who you are, and what's your place in this cruel world.

So nobody thinks it's Little Nemo the Dreammaster? Well, darn. ;p

Seriously, I'd tend to lean towards the Jules Verne idea, from the water imagery in the song - "soothing rain", "sailing home" and "compass" - the choice of words seems to imply the Captain Nemo interpretation. The 'nobody' interpretation works as well, though.

It was probably meant to be both. The more layers the better.

nemo is also "omen" backwards

Well, after reading through two pages of comments on "Nemo", I was more than vaguely disheartened that NO ONE (pun intended) picked up what this song is referencing. Yes, we all know that Captain Nemo's name is a reference to the existential loneliness that his character experiences, but Jules Verne was almost certainly referencing a far older work when he picked out his captain's name, in fact the 'name' that he picked was used by one of the oldest and most well known captain-heroes in all of literature, Odysseus.
For those unfamiliar with the Odyssey, 'no one' or 'no man' is the alias that Odysseus uses to trick the cyclops Polyphemus and thus enable his escape. For the details, read the Odyssey, (it is good, I promise... that is why it has been around for ~3000 years.) Here is a good explanation of Odysseus's encounter with the Cyclops and the pun on his name that is lost in translation:
en.wikipedia.org/wiki/Odysseus

Obviously "nemo" means 'no one' in Latin, so why wouldn't they have just used the Greek word (Ουτις) that Odysseus would have used?  The thing to keep in mind is that much of ancient Greek literature was handed down to Western civilization somewhat indirectly through the Roman Empire, which of course spoke Latin.  As a result, a lot of the more famous phrases from ancient Greek history were memorialized most famously not in Greek, but in their Latin form.  "Nosce te ipsum" the motto of the Oracle of Delphi is the famous phrase for 'know thyself', although the motto inscribed at the Oracle would certainly have been in Greek, not Latin.  
Thus, "nemo" is the word that (non-Greek) people will likely pick up on what it is referencing more quickly than "Ουτις", (and Tuomos may have purposely been making a reference both to the Jules Verne novel and the Odyssey, who knows but him?)   

If you have any doubts about my interpretation, bear in mind that Nightwish makes more straightforward references to the Odyssey in some of their other songs, like "The Siren".

Nemo is the capitain of Nautilus, the submarine from Jules Verne's 20,000 Leagues Under the Sea... And this is a song about loneliness...

Nemo is also latin for 'Nobody' or something similar.

'Nobody, my name for evermore' Whilst I agree with the Jules Verne comment, I think this is used as well.

oh my this is truely one of the all time best songs...the music is amazing..i saw it and my mouth was hanging open for like 10 minutes..this song is i think about a person who is alone..but wishes to liek be brought back to life..and is trying to find out the path to take to get out of the dark..Tarja is like so fircking awesome..i LOVE her! as a singer o/c

I think the name Nemo is a symbol of free will, the sea traveling is often used as metaphor for a free life with no bounds to anything.

The one without a name is the one without a purpose, without a goal in life, without a compas. The flower of the dreams of young age is used now only as a display of that time but a flower in a book is dead. So our man (or woman) must find what to do in life, must find a name. The name is Nemo, the seaman, the free, the man who is not belonging to anyone and anything. So, is time to sail to the seas of freedom.

P.S. As for some who think that their lyrics are bad i must remind them that nightwish is not a pop band with lyrics for brainless people. Use your head!!!