i made a thread about this a while back. the answers were scattered but i think we got it down to a source, although it is sketchy. LINK to thread
here is the best answer (given by Rush who said hippysmacker wrote this):
This is probably gonna bum you out, but it actually stems from the Auburn Tigers college fans rally cry. It was made a part of pop culture by Jim Rome on his radio show. Having observed this phenomenon while it was happening it always makes me smile when someone throws out " war" anything . Rome was in Alabama for the Auburn/Alabama game and he noticed everyone said " war eagle " right after goodbye or have a nice day. He said they said it in such a normal tone of voice that he realized it was a part of daily life for everyone. He told the story on the air, and fans started saying war" the cowboys" or chicks with big cans" ,or whatever they supported at the end of their calls and e-mails . 6 months later a guy at my work , who I know doesn't follow sports at all, threw out " war Milanos" when my boss said he was buying us free lunch from there. I knew it had spread ,and I had witnessed this with a lot of other pop culture phenomenons . Since Auburns team is the " Tigers' and Alabama are the " crimson tide" I was curious where war eagle came from . Heres a updated link to anyone who is curious what the phrase that started it all means. Svartom, as you are a fan of military history , I am sure you will appreciate this. For those of you who just want the short version.
War Eagle = The 2 words that a WW 2 Alabama American Army Captain most thought described " Pure American Glory" and he carved them on the Great Sphinx of Giza Egypt right before his troops went to a battle against the Nazis. A lot of fans say it's stands for " ever to conquer, never to yield"LINK