There are three types of variable data files to backup:

Couch-users discussion from Damien Katz - August 2008:

Actually, you can copy a live database file from the OS at anytime without problem. Doesn't matter if its being updated, or even if its being compacted, the CouchDB never-overwrite storage format ensures it should just work without issue.

For all platforms, locate your database, configuration, and log files and perform a filesystem copy. Be careful to preserve file permissions, too. Archive these files to wherever you want-- ideally on a different machine in a different physical location -- with appropriate security limiting access.

For example, here are the directories to backup for a CouchDB install on Ubuntu:

Note: Before CouchDB 1.0 intermediate releases can have incompatible database file formats. For details on migrating those, see BreakingChanges.