How to Save Tomato Seeds

Tomatoes are considered an inbreeding crop and many self-pollinate. You can typically grow several varieties in your garden and won't have to worry too much about different varieties crossing, especially if you separate them in different areas of the garden or plant a barrier crop, like corn or pole beans between them. Bees typically focus on pollinating one crop type at a time. They also like to fly in straight lines, when they fly up over the tall crop they will miss the plants below them on the other side. If you planted two different varieties next to each other, you can still save the seed. You may want to look at the flower and see if it is closed or open at the end and don't save from double bloom tomatoes as they are almost always open due to the weird configuration of the double bloom.

This is a picture of a double bloom the stigma is exposed for cross pollination, so avoid saving seeds from a double tomato when you harvest.

This is a picture of an exposed stigma which would easily cross pollinate as well. Space these plants farther apart from others if possible.

This is picture of a mainly closed flower. Although you can still barely see the stigma this tomato will likely self-pollinate. 

 This is an example of a totally enclosed stigma. There appears to be no chance that this will cross-pollinate.

1. Plant at least six or more plants and save tomatoes from the best plants. Even though tomatoes are inbreeding and typically self-pollinate, they have many polygenic characteristics that may drift over time if there is no selection pressure. Save seeds from several tomatoes just in case that one tomato was crossed you won't lose the variety. You should select for yield, quality, suitability, and horizontal resistance as described in Raoul Robinson's book Return to Resistance. Don't save seed from defective or odd plants. 
2. When you are harvesting ripe tomatoes take some of the pulp, juice, and seeds from the selected plants by squirt, squeezing, or scooping it into a sealable sandwich bag.
3. Close the bag and leave it in the cupboard for 3-5 days to ferment (rot) to kill off any pathogens that may be present in the fruit like Tobacco Mosaic Virus. This fermentation and rotting is similar to the natural process that occurs in the wild. Don't forget about it indefinitely...you know what I mean.
4. After three days fill the bag with water, pour of the pulp, the good seeds should sink (don't pour out the seeds). Any unfertilized seeds should float and get poured out with the pulp. If you lose a few in the floating pulp, that is probably okay. You should have more seeds than you can plant. Refill the bag with water and pour off the remaining pulp a few more times. There should just be a bit of water remaining on the seeds.
6. Invert the plastic bag, dumping the wet seeds onto a glass or plastic plate to dry (don't put them on paper towels or napkins as they will dry to them like glue). Carefully pour or blot off any extra water to speed drying. Put the plate in an empty cupboard or cabinet out of the way.
7. Let them dry for at least a week and then test the dryness by breaking one of the seeds if they dry and show not evidence of dampness you can dry them for longer or put them into bead bags or old glass bottles for next year.

Here is a picture of a German Queen tomato plant growing in a hay bale.

Hint: Lightly shaking or tapping your plants daily will encourage pollen shedding and self-pollination. This will ensure fruit formation even in the absence of a pollinator, e.g. in a greenhouse.