Estimation methodologies for SharePoint can vary based on the size, complexity of the project.
Books related to effort estimation methodologies in general or SharePoint in particular. Add books' link here.
Articles related to effort estimation methodologies in general or SharePoint in particular. SharePoint 2010 Best Practices http://social.technet.microsoft.com/wiki/contents/articles/8666.sharepoint-2010-best-practices.aspx
Other links for community resources SharePoint Design Patterns http://social.technet.microsoft.com/wiki/contents/articles/16884.sharepoint-design-patterns.aspx
Aalam Rangi edited Original. Comment: Adding link for Design Patterns wiki