What's the story behind Super Cow Powers?

Apt started its life around 1997 and entered Debian officially around 1999. During its early days, Jason Gunthorpe was its main maintainer/developer. Well, apparently Jason liked cows. I don't know if he still does. :-) Anyway, I think the apt-get moo thing was added by him as a joke. The corresponding aptitude easter eggs (see below) were added later by Daniel Burrows as a homage, I think.

If there is more to the story, Jason is probably the person to ask. He has (likely in response to this question) written a post on Google+. A small bit of it:

Once a long time ago a developer was known for announcing his presence on IRC with a simple, to the point 'Moo'. As with cows in pasture others would often Moo back in greeting. This led to a certain range of cow based jokes.

Also:

$ aptitude moo
There are no Easter Eggs in this program.
$ aptitude -v moo
There really are no Easter Eggs in this program.
$ aptitude -vv moo
Didn't I already tell you that there are no Easter Eggs in this program?
$ aptitude -vvv moo
Stop it!
$ aptitude -vvvv moo
Okay, okay, if I give you an Easter Egg, will you go away?
$ aptitude -vvvvv moo
All right, you win.

                               /----\
                       -------/      \
                      /               \
                     /                |
   -----------------/                  --------\
   ----------------------------------------------
$ aptitude -vvvvvv moo
What is it?  It's an elephant being eaten by a snake, of course.

I always assumed that this feature derived from cowsay & cowthink. See the Wikipedia article on Cowsay. I've been using these for years on Fedora (I believe they predate 1999) and were used as a way to display fortunes in a more interesting way.

$ fortune | cowsay
 ________________________________________ 
/ It doesn't matter what you do, it only \
| matters what you say you've done and   |
\ what you're going to do.               /
 ---------------------------------------- 
        \   ^__^
         \  (oo)\_______
            (__)\       )\/\
                ||----w |
                ||     ||

You can also use either of these to pass your own strings:

$ cowthink 'I love Fedora, Debian? Not so much!'
 _____________________________________ 
( I love Fedora, Debian? Not so much! )
 ------------------------------------- 
        o   ^__^
         o  (oo)\_______
            (__)\       )\/\
                ||----w |
                ||     ||

It also includes the ability to use alternate .cow files so you can swap other ones in, in place of the cow, such as tux.

$ cowthink -f tux 'mmmmm....Fedora!'
 __________________ 
( mmmmm....Fedora! )
 ------------------ 
   o
    o
        .--.
       |o_o |
       |:_/ |
      //   \ \
     (|     | )
    /'\_   _/`\
    \___)=(___/

I believe this comes a long way, from the "pre-http" era. Either Usenet, or even BBSs. Maybe as early as around 1987?...

I remember that there was tons of ascii-art circulating in the early days of Usenet. And IIRC in one of them it started to feature a cow, then some other posts featured more cows, then a post was entirely dedicated to several cows ascii-arts. I believe this easter-egg comes from someone reading those at that time...

I did a few seaches and found out a geocities page talking about it. That page states (excerpt:)

Besides digrams and charts, probably the earliest ASCII art from the Internet
are the "Spy at the Wall" collection and the "Silly Cows" collection.
David Bader, an ASCII art enthusiast and editor of the 'Cows",  recently sent
me the COMPLETE, UNCUT, ORIGINAL, and OFFICIAL Silly Cow collection!
These cows can be seen all over the Internet and are truly considered to be
"classic" ASCII art.. 

with "Silly cows" linking to : http://www.geocities.com/spunk1111/cows.htm (also available on the Internet Wayback Machine at : https://web.archive.org/web/20131225210911/http://www.geocities.com/spunk1111/cows.htm , or go rather to https://web.archive.org/web/*/http://www.geocities.com/spunk1111/cows.htm and click in the agenda below on the day of the Snapshot you want to see...)

Of course a true reference lies in usenet archives, but I don't have much time yet to do proper research (I may update this post in the near future)

At some point there was even a alt.cows.moo.moo.moo newsgroup created (probably quite a bit after cows started to invade ascii arts? But maybe before, I lack time to research properly) (see for example : http://www.418-teapot.com/topics/usenet/ )

To prove how popular it was in Usenet, the first question mentionned on the Internet Oracle wikipedia page: http://en.wikipedia.org/wiki/Internet_Oracle is about cow(s).