I�m thinking about to build an 500 NE on a Ruger#1 but i don�t know if I shall choose 500 NE 3" or 500 NE 3.25". What is the difference except a longer case? The most reamers for sale is for 500 NE 3".

Speaking of the 500 3" I have to sell my personal 3 die set that includes a trim die. They list for 169.00 I will sell mine for 135.oo and pay shipping in the lower 48 states.
George

I believe the 3 1/4 case is originally BP.

The .500s, in both case lengths, were originally black powder expresses. The Nitro versions were both generally loaded with 80 grains of Cordite and a 570 grain bullet. The only advantage that the 3 1/4" case would offer would be slightly lower pressure, nothing else. This is probably why the 3 1/4" was never very common. The 3" would probably be the best way to go.
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"Serious rifles have two barrels, everything else just burns gunpowder."

I went for the 3" after careful consideration of reamer availability, dies, the more fragile brass @ 3.25", avaiability of factory rounds in a pinch. The minimal decrease in pressure was not worth the extra hassle.

I chose the 3" due to ammo availability and so that I would not need to use a filler to take up the extra case space.

However, in a Ruger No. 1 you could load a 3 1/4" up with more powder, avoid filler, and get more velocity.