When you emerge a new package, etc-update will check if there are updates to the configuration files and will allow you to keep, merge or delete these files according to your needs.
Portage provides us with another useful tool with more functionalities: dispatch-conf.
dispatch-conf has the same goal than etc-update: manage the configuration files after merging, but provides new useful features:
- Ability to rollback changes
- Automerge files
- Versioning (rcs/cvs)
- Log changes
More info:
- man dispatch-conf
- GentooWiki