Below are the few Audit checklists which helps in Securing the WebApplication.

http://msdn.microsoft.com/en-us/library/aa302332.aspx
https://blogs.sans.org/it-audit/checklists/web-application-audit-checklist/
http://www.owasp.org/index.php/Category:OWASP_Testing_Project
https://www.watsonhall.com/methodology/checklists.pl
http://www.bestsecuritytips.com/xfsection+article.articleid+169.htm
http://www.certifiedsecure.eu/checklists/cs-basic-web-application-audit.pdf