Just the military as far as I know.

As I was pondering your question, crystal structures came to mind. Possibly snowflakes that happen to turn out to have right triangles as part of their structure. Other than that, I would suppose perhaps only at the atomic or subatomic level. I'd be interested to see some other repsonses.

Well, in the sense that anything in nature is "made", some crystals have right angles.

Oops, someone already noted that.

Water crystals in snowflakes do not make right angles, but instead make 60-degree angles, IIRC.

A spider may weave a right angle into its web. Of course, this strategy is employed by only the most elite of arachnids whose intelligence surpasses the stealth and stunning manuevers of most flying insects.

Oh, I LOVE spiders and I think you are correct in the possibility of right angles in a web. How about the veins in a leaf or branches to a tree? Or maybe a cactus of some kind? I know it is not the norm, but I think it probably occurs. Also, if a moth is resting on like a wall or something, it could form a right angle it that position.

I am sure on a molecular level it exists.

I don't know about right angles but i do know that the game of baseball presents a scientific problem dealing with circles and right angles:

How is it that the game can be played with the premise that you take a round bat and try to hit a round ball squarely?

Ouch, my head hurts now.