How do you handle the finances of a project?

I have a bunch of questions about the general financial aspects of a commissioned project and would love to hear how you all handle them. What have you found that works or doesn't work?

It is my top priority to 100% fair and honest to both myself and my clients so we both feel like we get what we wanted once the project is said and done.

Specifically, I'm interested in the following kinds of details:

1. Generating a quote - What factors do you include? How do you split things up? How do you itemize the task? Do you charge per-glyph? By the hour? Per feature set? Per language?
2. Getting paid - Do you stick to the quote price or do you require some pricing flexibility if the project changes (e.g., if it takes more/less time than you anticipated)? Do you require payment up-front, either in-full or an initiation portion? Do you ask for a lump sum at the end? Do you consider financing options for the client (i.e., breaking up the total into monthly payments with interest)?
   

Or, do you do something completely different? I'd love to hear your success and horror stories.