Once you get into using SharePoint, you get an idea of how big it is.
At that point you start to come across some questions of what’s the best way to do something.
I found a great article of some lessons learned about SharePoint.
These aren’t best practices, but more along the lines of tips.
The only tip I might add, is not to think before you create a new site. Only create a new site if you need all of it.
I have seen many times people create multiple sites, when they only need a couple of lists/libraries.
So ask yourself about if you are really going to need a whole site for what your doing.