I don't think there is a "best" way, but I just finished building my first one and can tell you a few things I would have done differently. I built mine out of mostly scrap lumber and an old wooden fence someone let me have. I used the fence boards for my siding. If I build another there are a couple of things I would do differently:
1. I would probably build it with a "shed" type roof instead of a gable- much easier.
2. I would build it bigger. Mine is 6x6', but the time and money wouldn't be much more to make it 8'x8' or even bigger.
3. I used 2"x4" welded wire or cage wire for my run. It is much stronger than 'chicken wire', however young chicks can run right through it! I learned this the hard way and then wrapped regular chicken wire around the bottom to keep them from running out.
4. Plan out where you want your roost, feed/water, nesting boxes and storage before you begin. Also decide where your run will be in relation to the coop and plan for the "pop hole" for the chickens into the run accordingly.
5. Do it as cheap as you can!
I used the plan found here:
http://www.buildeazy.com/chicken_coop_1.html
and modified it to fit my needs. Here are a couple of pics of the finished product. Good luck!