The Checklist

[+] Information Gathering

Manually explore the site
Spider/crawl for missed or hidden content
Check for files that expose content, such as robots.txt, sitemap.xml, .DS_Store
Check the caches of major search engines for publicly accessible sites
Check for differences in content based on User Agent (eg, Mobile sites, access as a Search engine Crawler)
Perform Web Application Fingerprinting
Identify technologies used
Identify user roles
Identify application entry points
Identify client-side code
Identify multiple versions/channels (e.g. web, mobile web, mobile app, web services)
Identify co-hosted and related applications
Identify all hostnames and ports
Identify third-party hosted content

[+] Configuration Management

Check for commonly used application and administrative URLs
Check for old, backup and unreferenced files
Check HTTP methods supported and Cross Site Tracing (XST)
Test file extensions handling
Test for security HTTP headers (e.g. CSP, X-Frame-Options, HSTS)
Test for policies (e.g. Flash, Silverlight, robots)
Test for non-production data in live environment, and vice-versa
Check for sensitive data in client-side code (e.g. API keys, credentials)

[+] Secure Transmission

Check SSL Version, Algorithms, Key length
Check for Digital Certificate Validity (Duration, Signature and CN)
Check credentials only delivered over HTTPS
Check that the login form is delivered over HTTPS
Check session tokens only delivered over HTTPS
Check if HTTP Strict Transport Security (HSTS) in use

[+] Authentication

Test for user enumeration
Test for authentication bypass
Test for bruteforce protection
Test password quality rules
Test remember me functionality
Test for autocomplete on password forms/input
Test password reset and/or recovery
Test password change process
Test CAPTCHA
Test multi factor authentication
Test for logout functionality presence
Test for cache management on HTTP (eg Pragma, Expires, Max-age)
Test for default logins
Test for user-accessible authentication history
Test for out-of channel notification of account lockouts and successful password changes
Test for consistent authentication across applications with shared authentication schema / SSO

[+] Session Management

Establish how session management is handled in the application (eg, tokens in cookies, token in URL)
Check session tokens for cookie flags (httpOnly and secure)
Check session cookie scope (path and domain)
Check session cookie duration (expires and max-age)
Check session termination after a maximum lifetime
Check session termination after relative timeout
Check session termination after logout
Test to see if users can have multiple simultaneous sessions
Test session cookies for randomness
Confirm that new session tokens are issued on login, role change and logout
Test for consistent session management across applications with shared session management
Test for session puzzling
Test for CSRF and clickjacking

[+] Authorization

Test for path traversal
Test for bypassing authorization schema
Test for vertical Access control problems (a.k.a. Privilege Escalation)
Test for horizontal Access control problems (between two users at the same privilege level)
Test for missing authorization

[+] Data Validation

Test for Reflected Cross Site Scripting
Test for Stored Cross Site Scripting
Test for DOM based Cross Site Scripting
Test for Cross Site Flashing
Test for HTML Injection
Test for SQL Injection
Test for LDAP Injection
Test for ORM Injection
Test for XML Injection
Test for XXE Injection
Test for SSI Injection
Test for XPath Injection
Test for XQuery Injection
Test for IMAP/SMTP Injection
Test for Code Injection
Test for Expression Language Injection
Test for Command Injection
Test for Overflow (Stack, Heap and Integer)
Test for Format String
Test for incubated vulnerabilities
Test for HTTP Splitting/Smuggling
Test for HTTP Verb Tampering
Test for Open Redirection
Test for Local File Inclusion
Test for Remote File Inclusion
Compare client-side and server-side validation rules
Test for NoSQL injection
Test for HTTP parameter pollution
Test for auto-binding
Test for Mass Assignment
Test for NULL/Invalid Session Cookie

[+] Denial of Service

Test for anti-automation
Test for account lockout
Test for HTTP protocol DoS
Test for SQL wildcard DoS

[+] Business Logic

Test for feature misuse
Test for lack of non-repudiation
Test for trust relationships
Test for integrity of data
Test segregation of duties

[+] Cryptography

Check if data which should be encrypted is not
Check for wrong algorithms usage depending on context
Check for weak algorithms usage
Check for proper use of salting
Check for randomness functions

[+] Risky Functionality - File Uploads

Test that acceptable file types are whitelisted
Test that file size limits, upload frequency and total file counts are defined and are enforced
Test that file contents match the defined file type
Test that all file uploads have Anti-Virus scanning in-place.
Test that unsafe filenames are sanitised
Test that uploaded files are not directly accessible within the web root
Test that uploaded files are not served on the same hostname/port
Test that files and other media are integrated with the authentication and authorisation schemas

[+] Risky Functionality - Card Payment

Test for known vulnerabilities and configuration issues on Web Server and Web Application
Test for default or guessable password
Test for non-production data in live environment, and vice-versa
Test for Injection vulnerabilities
Test for Buffer Overflows
Test for Insecure Cryptographic Storage
Test for Insufficient Transport Layer Protection
Test for Improper Error Handling
Test for all vulnerabilities with a CVSS v2 score > 4.0
Test for Authentication and Authorization issues
Test for CSRF

[+] HTML 5

Test Web Messaging
Test for Web Storage SQL injection
Check CORS implementation
Check Offline Web Application