One of the hardest things in running a small programming agency or doing freelance programming work is knowing exactly what to charge. When you are doing something which is essentially creative work and when you know from experience that the customer is going to change their minds about things as you go and you will discover unexpected problems along the way, it's very difficult to decide in advance what to charge for a project.
The guys over at a Web design agency called Blue Flavor wrote up a great post about how they put together their pricing packages and how they find the right price point together with their clients. What they are dealing with is graphic design and user interface, but it holds true for back-end programming as well. These are the same basic principles that I have been following for a while now, but some of their suggestions will certainly help me to refine my own pricing methods to make them better for both the client and myself.
One thing they say right at the beginning I think is key: "...honesty and transparency must be at the heart of pricing a project." Absolutely. Spot. On.