I installed JIRA on a hosted Windows server that was running IIS and other web sites on port 80. I needed to expose JIRA on a port that was open to the firewall (i.e. port 80) and using a URL that customers would find friendly, such as http://support.mycompany.com/jira. I walked through these two docs:

http://confluence.atlassian.com/display/JIRA/Configuring+IIS+with+Tomcat
http://confluence.atlassian.com/display/JIRA/Integrating+JIRA+with+IIS

but I still had several major issues that prevented the site from working. Please add these steps and troubleshooting items to your IIS integration docs:

A) Grant Windows ACL permissions to the c:\tomcat_iis_connector folder. Right-click the folder, go to the Security tab, ensure that you grant Full permissions for the IIS_WPG group (or the Identity used by the Application Pool if it does not belong to the IIS_WPG group). Then click the Advanced button and select this option: "Replace permission entries on all child objects with entries shown here that apply to child objects". Click OK.

Troubleshooting: Ensure that you perform step A if you have any of the following problems:
1) The ISAPI Filters tab shows a red arrow for the isapi_redirect.dll filter added earlier.
2) You receive a blank response from your custom URL (http://support.mycompany.com/jira)
3) A log file is not created within the c:\tomcat_iis_connector folder when you restart IIS and access your custom URL.

B) After creating the "jira" virtual directory, grant the Windows ACL Read permission to the Internet Guest Account (typically IUSR_servername) or whatever identity you have selected in your web site Directory Security for anonymous users.

Troubleshooting: If you receive an HTTP 401 (access denied) error from your custom URL (http://support.mycompany.com/jira) then ensure that you have done step B.

Troubleshooting: If JIRA responds on your custom URL (http://support.mycompany.com/jira) you may see the following error for each of the gadgets: "Error loading gadget: org.apache.shindig.gadgets.GadgetException: Unable to retrieve gadget xml. HTTP error 500". This occurs when the JIRA server is unable to resolve the domain name of your custom URL. If your server is hosted or for some other reason cannot resolve support.mycompany.com, then add the following entry to the C:\WINDOWS\SYSTEM32\DRIVERS\ETC\HOSTS file: 127.0.0.1 support.mycompany.com