Science: Draw a diagram of the western and eastern horizon views from your house—west on one edge of the paper, east on the other. Make 52 copies. Once a week, plot on your diagram where and at what time the sun rises and sets, and note the date. Kept in order in a notebook, this provides a good visual of the seasonal changes.
Choose a plant—a tree or shrub or even a weed if you're sure it won't be destroyed. A plant from the child's own garden is ideal. In a sketchbook draw the plant once a week all year, or for the life of the plant. Make note of significant events such as weather changes, hail, rabbit attack, etc.
On a calendar, keep notes of things you observe in nature: first meadowlark song of the season, sightings of various wildlife, etc. The children will become increasingly observant. You can compare this year's calendar to previous ones for some interesting insights.
Math: Any time a small child can use a calendar, money, thermometer, measuring devices, scales, etc., you are helping him with math. My children literally lived with those things as toys, and then when I thought it was time to put them in a formal math book, they already knew everything through the second grade level.