With the mustard seed, He talks about how the smallest of seeds can still bring about a massive tree. In a similar way, a massive religion is being formed from His own teachings. For a community of believers who saw themselves as such a small group compared to the world, this was a promise similar to the one that God gave to Abraham about being the father of many nations.
The yeast and the dough also talks about the power of a few to bring about change in many. The little bit of yeast allows for all of the dough to rise as it is mixed with it. In the same way, Jesus will send out his disciples into the world to spread His Word, raising the rest of the world as people learn and practice His teachings.
It is this mixing that is mentioned in the parable of the wheat and the weeds. As pointed out by our pastor in his homily, these weeds are specifically mentioned as being "tares"--a weed which looks much like wheat in its early stages and whose roots intermix and bind with the healthy wheat. The landowner in the parable refuses to have his servants pull out the tares out of concern that doing so will damage the wheat, but instead waits until harvest to separate them.
Many people, such as stated in today's homily, correctly take this as a analogy for why the Lord allows evil to exist in the world. Even the disciples clearly believed this was the meaning and were concerned about the meaning of the wheat and the weeds. They knew that they were not the purest of people, and worried that this message might mean they were doomed to the fire.
However, Jesus' explanation to them, especially when taken in context with the other two parables, shows that this is a message for His Church. In His explanation, He does not say the sower is God the Father, but rather "the Son of Man"--a phrase for Himself. As His teachings spread, there will be people who take and distort His message. Like the tares, they will seem to be good on casual inspection, but they will be entwining their hidden intentions into those of Christian teachings, trying choking them out. Yet Jesus has not smited those who have twisted His message, for doing so would harm the good with the bad. Instead, He will still bring about good works in the end despite those who have tried to work against Him.
These parables are messages of hope. They speak to the spreading of good in the world. They tell us that small actions can bring about greater effects. Most importantly, they inform us that, despite the deliberate attempts to sabotage His Word, the final harvest will clearly demonstrate that good triumphs over evil.