Lycopersicon are members of the Solanaceae family.
Lycopersicon self-pollinate (for the majority of varieties) although it is possible for tomatoes to cross-pollinated. Some ancient and heirloom varieties have long, protruding styles will cross with other varieties with the same protruding styles.
Since Lycopersicon are mainly self-pollinating, 5 feet between rows containing different varieties of the same species should be sufficient if you are growing the modern varieties. But, in order to preserve the genetic diversity of the species, a minimum of 100 plants should be grown of each variety for seed production. If you are growing varieties with long, protruding styles, plants should be isolated like any other cross-pollinated species, with a minimum of 1/2 mile between same species varieties.
Tomatoes should be harvested when they are fully ripe.
Tomatoes can be processed manually or mechanically. I use a Millett's Wet Vegetable Seed Separator to clean tomatoes but, this process can be done simply by cutting the tomato through the middle and squeezing out the seeds into a container (See picture to right). After all the seeds from one variety are in the container, add as much water as you have seeds and ferment for 1 - 3 days (stirring twice a day). During this time you will notice a pungent odor coming from your bucket and a thick mold layering the top of the mixture. Once this mold completely covers the top, the seeds should be ready. The viable seeds will sink to the bottom and you can discard the rest of the mix. If you pour off the top mold and some water, you will notice the viable seeds left in the bottom. After you pour off the mold, refill the bucket with clean water, let settle and pour off remaining debris. Continue to do this until all the debris is gone. Place remaining seeds in a mesh bag and dip into a 20% Bleach solution (1 cup Bleach to 4 cups water) for just long enough to make sure solution has contact with all seeds (this will protect against Tobacco Mosaic Virus). After dipping the seeds, place on a screen to dry. You may want to rub the seeds while they are drying to avoid clumping and to remove the tiny hairs found on the seeds.