When collecting seeds in your garden, look for healthy plants that possess the characteristics you desire. For instance, if you have a pot marigold (Calendula) with a pale apricot color that you admire, collect seeds from the paler specimens to try and keep the nice shade. You will always get variation, but you are participating in the selection process as, in essence, an amateur breeder.
Always choose healthy plants so that you end up with healthy, viable seeds. Don’t waste your time collecting seeds from F1 hybrids; they will never come true to seed, and you will get some strange results. Heirloom varieties, on the other hand, tend to be fairly stable and are wonderful to collect.
Gather seeds from your garden once the flower or vegetable has started to ripen. With flowers, the seed heads will start to turn brown. Harvest your seeds on a dry day; you will dry them anyway before you store them, so it helps to get a head start and to ensure they don’t rot during the process.
It is essential not to collect immature seeds. Many seeds will continue to ripen as they dry, but if you collect them before they have completely formed, they will not mature and produce viable seed. They should be fully formed and starting to dry.
With fruits and vegetables, the fruits should be just starting to get over-ripe.
There are exceptions to this timing rule; many seeds are catapulted into the air or the inflorescence (the seed head) shatters to help the seeds disperse effectively in the wild. These seeds should be harvested just before they are ripe so that they are easier to collect, otherwise, they will explode as you try to remove them. Place the entire inflorescence in a small paper bag and cut the stem.
Cut off the seed heads and collect in plastic containers or paper bags. Make sure you label everything as you go. If you wait until you can spread everything out to identify your seeds, you will be give yourself an unnecessary headache. Record the collection date and the cultivar name. Once gathered, the seeds will need to be cleaned and dried before they can be stored.
Some seeds require only minimal cleaning while others seeds have chaff or are in fleshy fruit and it is important to clean off these seeds so they will germinate properly. Seeds may be separated from the chaff (the seed casings and debris) with a pair of tweezers; not all of the chaff needs to be removed, but just cleaned off a bit.
A simple way to separate chaff from seeds is to make a deep crease down the center of a piece of paper. Place the unclean seeds in the center, tilt the paper at a slight angle and slowly tap the contents out of the folded paper (very similar to what you do when sowing seeds). The contents will separate, with the heavier items moving down the crease faster than the lighter items. If the seeds are heavier they will slide out first, and if they are lighter the chaff will fall out first. If the chaff and the seeds are close in weight the best thing to do is to find a screen that allows the seeds to fall through but traps larger pieces of debris; an old tea strainer or colander works well.
Seedpods are traditionally placed in an old pillowcase and stepped on, releasing the seeds, which are then separated from the chaff. Or place the pods in a bag and crush the pods with a rolling pin.
To clean seeds from fleshy fruits, scoop out the contents and soak them in water. Once cleaned, remove the seeds from the water and dry them on a paper towel. Many people who are serious about collecting tomato seeds ferment the seeds to clean off the fleshy coating (refer to the tab “Cleaning Tomato Seeds” at the top of this page).
Spread the seeds on newspapers, in a cardboard box, or in an old telephone directory, and allow them to dry between one and three weeks.
Before storing your seeds make sure they are dry, otherwise they will rot. But don’t desiccate the seed (it is alive); you merely want to get rid of excess moisture and hold it in a dormant state until you are ready to grow it.
Seeds need moisture, warmth and light to germinate, so give them the exact opposite, a dry, cool, dark environment, when storing them. Place your seeds in an envelope or paper bag and seal them in plastic containers or glass jars. If you are not convinced that your seeds are dry, eliminate the airtight container step. Remember to keep the labels with the seeds.
Store the seed in a cool, dry place such as a corner shelf in the garage, basement, closet or in the back of a refrigerator. The ideal temperature for storing seeds is between 32°F and 50°F. The rule of thumb for storing seeds is that the temperature and the humidity levels should add up to less than 100%. This means that if the temperature is 50°F, the humidity has to be less than 50%. Both high humidity and high temperatures are catalysts for germination and will trigger the seeds’ metabolism.
Photo courtesy of Flickr cc/MICOLO J Thanx 4
Beginning Seed Saving by 
The Complete Guide to Preserving Your Own Seeds for Your Garden by 
The New Seed Starter's Handbook by 
A Manual for the Identification of Plant Seeds and Fruits by 
