Remember the adage "What you reap, so shall you so." Well, that can be taken quite literally in the world of seed saving (with the exception of plants that easily cross-pollinate like the "easy" and "difficult" seeds to save). If you harvest small tomatoes, you're likely to get small tomatoes. If you harvest the first tomatoes of the season, their offspring will be more likely to produce earlier in the season.
When choosing which seeds to harvest consider the following:
Ability to tolerate drought, wind or other extreme conditions
Ability to compete with weeds
Early-, mid- or late-bearing fruit (whichever is desired)
Long storage life
Late to go to seed or bolt
Good fruit texture
Resistance to insect pests
Larger fruit or flowers
After you save the seeds, make a note of why you chose these particular seeds, where you grew them, and when you harvested them. This process will help you to learn from your plants and to start creating the varieties that work best for your location.