Apple seeds, by the way, are also called "pips".
I agree with jmd in that it means "small unit" but I'd take it a bit farther (and a bit more obnoxiously) and call it a "small item".
Pip is synonymous with spot, speck, spick, et al - and also carries with it the term "pipsqueak", or someone/thing that is small and insignificant.
I'd think its base usage is the same as it is for dominoes - a tiny spot, or collection thereof, meant to designate a numerical value.
As for the origination of the term "pip", it might have something to do with the 18th c term "pippin", or a small, fleshy, small-seeded fruit, lending the derivative "pip" to its seeds, and therefore to the marks on dice/dominoes/cards.
Just my uneducated $0.02.
Illy