They are called "dog holes". The stick that you place in them is called a
"bench dog"
There should be a vise which also has one or more dog holes. A dog placed in
a fixed hole in the bench top used in conjuction with a dog in the vise
become the "jaws" of potentially large vise or clamp above the surfadec of
the bench.
You should be able to get the idea from the picture on this link
http://www.woodirect.com/workbench.htm


Off topic:

Stephen do you own this bench? It shows that the center wood top is 1 1/8" thick,
that should be 5/4 or 6/4 stock I think, but do you think it matters if the wood is
that thin? It seems to be a good deal compared to the Rockler $400 Sjoberg.

On topic:

I just bought 8 Lignum Vitae pen blanks to become bench dogs, they'll be fun to make!

Alex