Most efficient way to find smallest of 3 numbers Java?

No, it's seriously not worth changing. The sort of improvements you're going to get when fiddling with micro-optimisations like this will not be worth it. Even the method call cost will be removed if the min function is called enough.

If you have a problem with your algorithm, your best bet is to look into macro-optimisations ("big picture" stuff like algorithm selection or tuning) - you'll generally get much better performance improvements there.

And your comment that removing Math.pow gave improvements may well be correct but that's because it's a relatively expensive operation. Math.min will not even be close to that in terms of cost.

For a lot of utility-type methods, the apache commons libraries have solid implementations that you can either leverage or get additional insight from. In this case, there is a method for finding the smallest of three doubles available in org.apache.commons.lang.math.NumberUtils. Their implementation is actually nearly identical to your initial thought:

public static double min(double a, double b, double c) {
    return Math.min(Math.min(a, b), c);
}

double smallest = a;
if (smallest > b) smallest = b;
if (smallest > c) smallest = c;

Not necessarily faster than your code.