Looks like two things going on with this cutting. Shock from being severed from its stem and placed in a cup of plain water and possibly some bug damage too.

As to the toms in the jugs yellowing--they liekly need food. They should be in the ground ASAP. I plant my toms out when they barely have their true leaves. Getting them into the ground quickly means their roots start growing in the soil, they begin getting nourishment from the soil and through photosynthesis. PLant your seedlings, give them intitially a 50% strength feeding with any tomato-type plant food. Wait two weeks and feed them again. You should see an improvement within a week or two after planting.

In the meantime, use the link below to learn about tomato problems. Tomatoes do get various problems but they can be treated. I live on an island--humid air is a breeding ground for mildew, fungus and various blights. I do use an organic fungicide which does a great job at controlling the problems. It doesn't cure them, but it keeps them at a manageable minimum.

T

Here is a link that might be useful: TAMU Tomato Problem Solver