There is an excellent topic at Sphinn asking how do you price your SEO projects.
Overall, many charge flat rates based on how much they anticipate the project will cost them. But some charge hourly. Some charge by feature or service. Most charge monthly.
Let me quote some of the well known SEOs who describe how they charge:
Jill Whalen:
Julie Joyce:
Nick LeRoy:
How do you price your SEO pricing?
For me, if someone wants my SEO advice, I just bill them hourly. Although I rarely give SEO advice outside of this site.
Forum discussion at Sphinn.