The JIRA markup language / parser only recognizes HTTP-based URL's and URI's. If I try to embed links using other protocols, such as smb, file, or doors, JIRA markup fails to recognize them as legal links.

The workaround is to use HTML directly, but that defeats the purpose of the markup language, and the workaround doesn't seem to be universally supported on all JIRA versions.
NOTE: The workaround works fine on our installation of JIRA 4.3.2, but it doesn't seem to work on this version of JIRA. At least, the preview function isn't displaying it correctly.

Example: The following link will not be recognized by the JIRA markup language:
[Design Documentation on the MAC server|smb://DocumentationServer.internal/Public/MyMACProject]

Workaround: Bypass the markup language and use native HTML:
{HTML}<a href=smb://DocumentationServer.internal/Public/MyMACProject>Design Documentation on the MAC server</a>{HTML}

When I test the links above on this JIRA project, the HTML workaround doesn't seem to work on this version of JIRA. On our internal network, the blue link above not only displays the URL properly, but users can navigate directly to the directory location that is captured in the URL (assuming that they are on a MAC, which natively supports the SMB protocol).

FYI: The doors protocol, that I use as one of the examples above, is an example of using URL link that depends on an installed application. In this case, the application is DOORS, from TeleLogic/IBM. As long as the user has DOORS installed, and I use this workaround as part of how I markup the JIRA task description, users are able to navigate from the JIRA task, directly to the requirement description in the DOORS application.