There are several ways to join granny squares to make an afghan. The most traditional way is by whip stitching with a yarn needle. You can also join them with a row of slip stitches or single crochets. This will result in a more prominent seam. Lastly, you can get creative by joining them with chains and spaces to create a lace look.
I have always joined my motifs with slip stitches because it's very easy to take out of you make a mistake. The rainbow afghan below was joined this way. I joined in the back loops only which left the front loops to give each square an "edge."
It wasn't until recently when I was crocheting an afghan for my grandmother that I finally decided to try whip stitching. I had always been afraid that I would misalign the squares and spend hours taking out the stitches. But this was an important project and I wanted it to look as nice as possible.
So I held my breath, lined up my first two squares. I was so excited when it not only worked, but it looked great! I literally "whipped" through the rest and ended up with clean edges and no seams.
Tradition is formed many times because it really is the best way to get something done. From now on I will listen to my crochet ancestors!