If each tomato has one soft black spot on the bottom of the fruit, it's called blossom end rot. Treat by adding calcium to the soil; crushed eggshells are ideal. Then mulch so the soil will remain more evenly moist after watering or rainfall. If they are smaller black spots (1/4 to 1/2 inch) irregularly placed on the tomato's surface, it sounds like a disease. You can cut around the bad spots and still eat the tomatoes. Then remove all of the plant debris from your garden this fall so the pathogen can't overwinter and attack again next year. Moving your tomato planting to another spot for a season or two will help, too. Now, about the peppers and basil. I wonder if they're fairly recent transplants; sometimes new transplants can suffer shock and sunburn when they're new in a sunny garden.