This is where ERD comes into play. Its the diameter as measured from the ends of the spokes. Ideally, this corresponds to the ends of the nipples, but due to the vagaries of fortune, it doesn't always work out just the way we want. If the spokes stick out of the nipples a bit, it isn't a problem, especially if you have a double-walled rim.

As for calculators, most of them use the same math, so most of them end up with the same length. As long as you have measured your ERD correctly, you'll be ok. You did measure your ERD, right? :-).

(As usual, FBinNY beat me to the punch, and with a better answer).

An addendum: you can make ERD measuring devices by cutting two spokes to a known length (200mm works well) and screwing them into the nipples that you are going to use. Measure the gap (or overlap) between the spokes, add (or subtract) from the sum of the spokes, and you'll have an ERD that should be accurate for your nipples.