Is there a way to build thumbnails with a black box around them instead of cropping the image? Or the ability to produce thumbnails that maintain aspect ratio?

Putting boxes around thumbs is a CSS task. Several of the themes put boxes around them, but not, I think, black ones. Still changing the color to black should not be that hard.

Try reseting the crop thumbnails option on the options/image display tab. I am not sure what you are asking for, but this will keep the whole image, so the aspect ratio will stay the same.