Waterproof them as soon as you get home.  If your boots are made from leather, use an oil based product to waterproof them.  Stay away from waxes or silicones that can clog the pours and shorten the life of the boot.  Make sure to pay close attention to the welts at the mid-sole and to get a good amount of waterproofing material in those seams.  If your boots are synthetic, use a silicone based waterproof product.  Not only will oil based not work well, it can actually damage your synthetic boot.  Again, pay close attention to the welt seams at the mid-sole.  If your boot is a composite of both synthetic and natural materials, follow the manufacturers instructions.
 

Break your boots in before going hiking in them.  Wear them around the house, when going to the store, for a few days at work, any opportunity where you can soften up the sole and get the material to stretch a little to the shape of your foot.  Don't get caught on a trail in a new pair of boots that haven't been broken in.  There is not a set time period or distance for a break in of new boots, listen to your feet.  If you have gone for an extended period of time, or walked for more than ten miles and your boots are still uncomfortable, you may have to rethink your purchase.
 

Keep them clean.  When you buy your boots not only should you walk out of the store with waterproofing material, but you should also leave with an appropriate cleaner.  There are a number of products on the market today that will work on either synthetic or natural materials.  Start by banging your boots together to get the largest amount of dirt out of the lugs.  Then, take a stiff nylon brush and brush the boots to get the dirt off.  If your boots are still dirty, get a damp cloth and wipe the dirt away, be careful not to soak the leather.  If you are removing volcanic dust, use a vacuum and stay away from water.  Once you have cleaned them up follow the directions on your selected boot cleaner.  After cleaning your boots, you should waterproof them again.  Wait until they are fully dried from cleaning before repeating that process.
 

Never heat dry wet boots.  If you get your boots wet, don't place them by a fire or heater to speed up drying them off.  It only damages the material, effects the fit, and if you get your boots to close to the heat source, can melt the cement holding the sole to the upper.  Let them natural air dry in a warm dry place.  If you get a mildew smell, you can use foot powder or baking soda to get the smell out.  Once dry, give them a thorough cleaning and re-waterproof them according to the directions with the boot.
 

Don't store your boots for an extended period of time.  If you live in a cold climate, or only hike when you travel, don't let your boots sit unused for a long period of time.  Wear them periodically to keep them stretched out and comfortable.  Use them to run errands or around work if you get up and down.  By doing this you will keep the soles soft and the uppers comfortable for your feet.
 

Don't walk around with them unlaced.  This is a sure temptation when you reach your campsite, especially if you have been hiking for a long distance and you didn't bring camp shoes.  Walking around with your boots unlaced causes unnecessary wear on the inner linings and will shred your laces.  Invest in a pair of sandals, camp booties, or throw a lightweight pair of old tennis shoes in your pack for letting your feet relax.