Currently (as of 3.6 versions) Jira will only render urls as links if they use one of the protocols hard coded in the URL list.
If you wish for something else to be rendered as a link, such as Lotus Notes links which use the Notes:// protocol, you must manually add it to the list in the jira code.
In the /atlassian-renderer/src/java/com/atlassian/renderer/util/UrlUtil.java file,
change the list of URLs to include your protocol, such as Notes:// in my example below.
"http://", "https://", "ftp://", "ftps://", "mailto:", "nntp://", "news://", "irc://", "file:", "Notes://"
I did mention this in the forums or an email or something at some point, and someone from Atlassian responded by saying that they really should not be restricting any links using a hardcoded list and this should be changed in the future.