Calling all Spielfrieks! It's time to vote for the Meeples Choice Awards at the Yahoo User Group!
The source is a song from the late sixties rock musical "Hair". The song is "Aquarius" and its lyrics went, "This is the dawning of the Age of Aquarius". It referred to the hippie/free love/anti-war movement of the sixties. "Age of Aquarius" is an astrological term, meaning "age of love". The song was a huge hit, making the term Age of Aquarius somewhat synonymous with the late sixties.
That period was also known for its psychodelic imagery, like that used in the game Aquarius. The Looney's are kind of hippie-like in their beliefs, so I'm sure that had an effect on the title. But mostly, I think it refers to the game's graphics.