The short answer is "lighting."
Remember that traditional animation is constructed from multiple elements, layered and photographed together. Static elements such as backgrounds are painted on sheets of glass (plates) and moving elements such as characters are painted on multiple sheets of acetate (cels). Each frame of animation is built by layering the various elements in a photography studio, lit, photographed, and then re-built and shot again for the next frame.
Creating glow effects can be done by painting them by hand, but those super bright psychic auras, laser blasts, and the like take advantage of the fact that glass and acetate are transparent. By shining a light up from underneath the background, through translucent or unpainted portions of the various elements, or by directly cutting out parts of the cel with a razor, you can create anything from a soft, diffuse glow to intense, bright light. Color gels placed between the cel and the light source will give you those brilliant reds or blues (or oranges or purples or greens or whatever).
Lens flare and sundog effects are done in-camera by using studio lighting to create the desired glare on the lens itself.
Things get a little more complicated when you want to, say, add that intense glow to a fully painted object (like the glowing brick at the bottom there). For that, they would likely use an optical printer, a device that allows you to combine previously photographed elements with new optical effects or with other existing photographed elements. You combine the photographed sequence of the characters holding the brick, with a matte blacking out everything except the brick, and blue light shining through the brick-shaped hole in the matte, and the optical printer allows you to re-photograph those elements together, essentially.
The shot of the rippling water on the shore is also an optical composite, combining background elements (grass, tree), foreground elements (the character) a matte that blocks out the grass, tree, and character, and footage of the water effect, which may be filmed with actual liquid (heavily watered down shampoo was popular) or a stand-in medium (crinkled, reflective foil with a moving light source was also popular).
It's all effectively the same method ILM used to assemble all of the individually shot miniature X-Wings and TIE Fighters and Death Star trench footage in Star Wars.