This is a braindump. Expect change and refinement as I realize or am told where I'm wrong or what I've missed.
I'm planning a blog post on this (eventually), but wanted to start collecting / recording thoughts here. Basically, I've seen a lot of different ways to run a company over the course of my career -- both directly (by working in many different environments) and indirectly (through friends and companies publicly releasing their practices). As a result, it's been almost impossible to avoid creating a list of things that I'd do were I in charge of my own company.
I'm dividing this up into rough categories, but neither the format nor the content is set in stone.