I have complete database package that I charge a fixed prices. I compare my software to what is available on the market, such as what my software does better and then what my software does not do. Price based on the market price.
As far as by the job pricing it would depend on how technical the software is. If it has large complex calculation, that I have to do a bunch a research, then the price goes up. Do you have to travel doing research, setup, and training of your software. Other items to consider is how much experience do you have, the more experience the more your time should be worth. You also have to consider what others in your area may charge for the same type work. You will have to pay taxes on your profit at the end of the year. How much training do you have? Are also installing a network? Are you setup a brand new computer? Are you going to sell the buyer the code for the software or are you going to sell them a license just to use the software. If you are selling the code then the price would go up. I would charge around $100.00 an hour for most jobs and I only sell them a license to use the software. If it is a non-profit organization then my price may go down. Travel and overnight expense may be charged separately, just depends on the job and the buyer.
I start from an hourly rate, estimate the amount of time required to complete the client's project--after an an initial analysis phase to set the "project scope" and generate a "feature list" (and I include the time spent on this as part of the total project time. Then I quote the client a flat fee based on that rate. That way, I provide the user with both a detailed description of what will be done and a value that they can use to determine if they can afford me.
If they ask my hourly rate, I tell them, but also tell them that the figure is meaningless for cost comparison with other developers as the time for which they will be billed may vary by a very large margin so a high rate for few hours could easily be cheaper than a lower rate for more hours.
I only charge by the hour with no "cap" for long term clients (for whom I have earned their trust) and usually then only for additional requested features not part of the original estimate. And this is something that I warn clients about, that often when they see what Filemaker can do for them, it sparks ideas for even better/more features and those will not be covered in the original quote.