For one or two table tourneys, I prefer sets starting with either 1 or 5 (or appropriate multiples) because they allow four levels of standard chip denoms to be used without bumping into the 500/1000 problem -- i.e., all steps are multiples of 4 or 5.
Thus, starting with 25s as the smallest chip (i.e., at 25/50) is right out.
And I don't usually run tourneys with only 100BB to start -- generally at least 200BBs.
So 1 and 5 are fine, as are 1,000 and 5,000 -- but 100 and 500 are out, because 2,000 and 2,500 denoms don't commonly exist.
Personally, as the smallest chip, I prefer 5s to 1s, and 1,000s to 5,000s.
So starting at either 5/10 or 1000/2000, at 200BBs, means starting stacks of either 2,000 or 200,000, depending on whether you want it to feel like a normal casino game or a "high roller" tournament.
Hope that makes sense...