1. (from memory) Scale, roughness, blend mode & reseed
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2. No. Pens & pencils are for drawing not selecting. Use the Magic Wand to select irregular areas (tolerance will affect the selection area based on similar/dissimilar colors), the Ellipse and Rectangle selection tools select more regular areas.
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3. Blend modes change the result of pixels when overlaid. Check this link: http://www.getpaint.net/doc/latest/en/LayersAndBlendModes.html
4. Search for the "Primary Color Difference to Alpha" plugin.
5. Alpha = transparency amount!. The above link also explains this.
6. Boxes, spheres and cylinders. All customizable to your hearts content.
7. There are a number of fractal effects, mandelbrot, julia and (memory failure - dang, I thought I had another one...). This link shows where to find them (and clouds) http://www.getpaint.net/doc/latest/en/EffectsRenderMenu.html
Section for PDN art? Sure is, we call the the Pictorium, and it's part of this forum.