It is a reference to how children sometimes count on their fingers. It's an old, lame joke that if someone needs to count higher than 10 they can use their toes too. He's making that joke at himself.
While the sociologists are off figuring out why this gave us a base ten number system instead of base eleven, the computer scientists are showing off how they can count to a thousand instead.
(And also get thrown out of every bar where they order four of something.)
A base-12 number system would be advantageous because 12 is a "superior highly composite number". However, needless to say, despite the number theoretical advantages changing from our current base-10 system is essentially impossible.
Regardless of its origin, base 12 is still a major part of our lives (24 hours to a day, 60 minutes to an hour, even 60 minutes to a grade in angles).