The seedlings look great and I'd go ahead and pot them up.

I grew tomato seedlings in used paper coffee cups this winter, and I didn't think they were very good for bottom watering as the paper part of the waxed cup would soak up all the water and I wondered if the plants were getting enough water (although I did punch holes in the bottoms). I prefer to water from the top normally (which is not recommended), but I had a fungus gnat problem.

Linda

Thanks, Linda! To clarify, I'm mostly wondering if that "black mold" (or whatever it is) poses any kind of health risk to the plants or anyone enjoying their future bounty, or if it is simply something benign.

It is basically benign but it still shouldn't be ignored as it is a definitive sign that the soil in the cups is being kept too wet. It is easy to eliminate - and to prevent in the first place - but it poses not long-term threat to the plants. There is more of a threat to them from the overly moist media.

And they definitely need to be transplanted into individual containers before the roots become even more entangles and the transplanting kills them.

Dave