Question: How can I collect some of my heirloom pepper and tomato seeds and have them produce the same fruit?
Answer: The keys to saving any seeds is to avoid cross-pollination and to keep the seeds viable until you are ready to plant them.
Cross-pollination happens when a pollinator like a bee visits a plant of the same species, gets some of that pollen on it, and then visits the plant you are seed-saving from and the pollen gets on that flower. Now that seed will produce a plant that is a mix of the two varieties.
While this may not be a bad thing, it is not want you wanted. Seed saving is all about reducing the odds of cross-pollination from happening.
With tomatoes, this is easy because tomatoes have evolved in a way that they do not cross-pollinate readily. For most varieties, the flower has pollinated itself before it is fully opened and cannot now be cross-pollinated.
This is not as certain with tomato varieties known a potato leaf tomatoes, which cross pollenate a bit more frequently.
In either case, you can collect the seeds from over-ripe tomatoes and have a good chance that the seeds will produce the same variety of fruit when you seed them. To further reduce the odds of cross-pollination, I wrap the entire tomato cage in a lightweight row cover, which reduces the chances that a bee will find its way to the flowers.
Peppers are a totally different problem for seed savers. Peppers cross-pollinate in a garden about 75% of the time, so your odds of just collecting seeds without protection that will produce the same variety of fruit is low. The key is to reduce the chances that a pollinator will visit the flowers you want to save seeds from.
Some folks will fix a small net bag around an emerging flower to keep the pollinators away. These bags are available online. Personally, I have not had good luck with this technique. I prefer to build a cage out of ½ inch PVC pipe and cover it in a row cover to keep the pollinators away from the flowers. In this case, I recommend you give the plant a shake every week to make sure the flowers get pollinated.
One thing you have to be careful with when covering plants in row cover is that you are also excluding the beneficial insects. Aphids can become a major problem, as nothing is there to control them. I recommend introducing ladybugs under the cover. One introduction seems to be sufficient; they stay inside the enclosure and reproduce, controlling the aphid population.
Now that you have pure seeds, how do you collect and preserve them? This time peppers are easy. With the peppers, simply let the fruit completely ripen, harvest it, remove and enjoy the edible part, leave the seeds on the white pithy bit and let it dry for a few days. After a few days, remove the seeds, let them dry completely and store them in a cool, dry, and dark place until you are ready to seed.
Tomatoes are a bit trickier. Once again you want to let the fruit completely ripen, then cut the fruit crosswise and squeeze out the seeds. If you want to get all the seeds, you will have to dig around the fruit to find them.
You will notice there is a jelly-like substance around the seeds. This is a very interesting adaptation that keeps the seeds from germinating inside the fruit and increases the odds they do not germinate until the following spring.
If you just leave these seeds to dry as is, first they will all stick together in a mass that you will have to break up. Secondly, when you plant the seeds, they will have to ferment in the potting soil to remove the protective jelly before they will germinate, which will produce staggered germination times with some seeds germinating quickly and others taking longer.
To avoid this, I recommend you put the freshly harvested seeds in a glass of water for three days. In three days, you will have a glass of nasty, fermented tomato seeds. Clean the seeds in a strainer by running cold water over them to remove all the nasty parts, let them dry completely and store them in a cool, dry, and dark place until you are ready to plant.