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This page describes Atlassian's recommendation for installing JIRA and Confluence on the same server. Refer to Here Be Dragons for instructions on integrating all Atlassian applications.

Recommended Setup - Separate Stand-Alone Installations

Atlassian recommends running JIRA and Confluence in separate stand-alone instances running behind an Apache Web Server. See the guides for:

Advantages

Each application can be restarted without affecting the other.
If one webapp hangs for any reason (eg. running out of memory), it doesn't affect the other.
Any problems can be debugged more easily. Logs are separate and product-specific, rather than everything going to catalina.out. Thread and heap dumps are smaller and more relevant.
It reduces the likelihood of jar conflicts (eg. jars that must be installed in common/lib or lib for Confluence running off Apache Tomcat version 6 or above), particularly if you later want to install a third webapp not from Atlassian.
Apache HTTP Web Server is well suited for running publicly available sites, with extensive modules for security and efficiency. It also allows for flexibility with URLs (ie http://confluence.atlassian.com, http://confluence, and so on).

Apache Web Server is recommended and reliable. It is also a third-party product, and therefore not developed nor supported by Atlassian. See Atlassian Support Offerings for details.