Hi Patricia,
The tomato thing is easy to diagnose. It's a disorder called tomato blossom end rot (sounds painful!). It is caused by dry conditions around the plants' roots, which prevent the plant from taking up sufficient calcium. The low calcium content of the fruit causes the cells to collapse, starting at the base and spreading upwards. It can also be encouraged by growing in a soil or compost that is too acidic.
There is no cure for it, but you can try to prevent it from happening by ensuring regular, adequate moisture at the roots, rather than periods of dryness.
Pick off affected fruits to prevent further fungal or bacterial infection. The smaller, cherry-type tomatoes seem to be less susceptible to blossom end rot.
Your peppers are a different story. Is it the plants that are rotting at the bottom, or the developing pepper fruits? Can you give a little more detail on the rotting problem?
The holes are probably caused by some form of caterpillar (it is interesting that the hottest of chillis can still be attacked by caterpillars...it's almost as if the little pests have no sense that they're eating something that would bring tears to the eyes of even the toughest, most hardened chilli fan!). You can spray the plants with any caterpillar killer that is formulated for use on edible plants (such as Bio Liquid Derris -- which, being a natural insecticide, is also suitable for organic gardening).
I hope this helps.
Graham