For you BSG fans, we found out on Friday's episode "Someone to Watch Over Me" that (spoiler) Starbuck's dad knew the song "All Along the Watchtower," which was the song that brought four of the Final Five together, and was recreated by Boomer's daughter Hera in her drawings. I did a some research, and here are my interpretations behind why this song was chosen as the Cylons' national anthem, as it were.

First of all, here are the lyrics.

“There must be some kind of way out of here,”
Said the joker to the thief.
“There's too much confusion,
I can't get no relief.
Businessmen, they drink my wine,
Plowmen dig my earth.
None of them along the line
Know what any of it is worth.”

“No reason to get excited,”
The thief he kindly spoke.
“There are many here among us
Who feel that life is but a joke.
But you and I, we've been through that,
And this is not our fate.
So let us not talk falsely now,
The hour is getting late.”

All along the watchtower,
Princes kept the view,
While all the women came and went —
Barefoot servants too.
Outside in the cold distance,
A wildcat did growl.
Two riders were approaching, and
The wind began to howl.

The first thing to note is that most of this song is simply a conversation between two people, the Joker and the Thief. The Joker is the Human, and the Thief is the Cylon. In the first verse, the Joker laments his loss of land and wine.

This is reference to the plundering and destruction of Kobol, the original home of the Humans destroyed by the Cylons after their revolt. The Cylons purge Kobol out of pure revenge after years of slavery, not caring about what possibilities lie within the soil of the planet, and the Humans and human-like Cylons (Skinjobs), flee to find a new home.

The Thief, in the line “There are many here among us who feel that life is but a joke," refers to the Cylon Resurrection ships. Life is a joke if there is no penalty of death. No harm, no foul. But he goes on to say, "But you and I, we've been through that, and this is not our fate." This is a premonition of the destruction of the Resurrection Ship, and the Thief is essentially saying to the Joker "Yes, now we're all mortal, so now we must work together if we're to survive."

Then we get to the meat of the lyrics. "All along the watchtower, Princes kept the view." The watchtower is the external gate to the theoretical Promised Land that the Humans and Cylons are heading towards, but is barred by the Princes. The Princes are Cavill and the other Cylons that seek to destroy the Final Five.

"Outside in the cold distance, A wildcat did growl." This is the emptiness of space, the endless void that will envelop both the Humans and the Cylons if they don't find a place to call home.

"Two riders were approaching, and the wind began to howl." This line connects the first two verses to the third. The two riders are the Joker and the Thief. The Human and the Cylon. At the end of their journey these two people, who have very little interest in dealing with each other, are forced to work together (Galactica and the Basestar), to find a suitable home for both of them.

This link is an excellent version of the timeline of BSG, and helped me form this theory. It might not cover all the bases, but it helped me understand the plight of the Humans and Cylons a little bit better.