First off, create a backup before changing anything.
Sometimes the config files are installed by your package manager, whichever you use, and you can query its database, but I wouldn't rely on that. For some distributions there may be tools like findcruft (now abandoned) for Gentoo.
I think your best chance is to find and remove the files that haven't been accessed for a longer period, but this is no guarantee that the package isn't installed but inactive. Bonus points for checking the candidates against the package manager in a script.
$ find /etc -atime +7 Be aware that not all file systems support the atime feature, or it may be switched off intentionally, e. g. for SSD drives. In this case you can't use this approach. Or you'll first have to switch atime on for a decent period to gather the access data in order to make reliable decisions. Read about the relatime option first, too.
$ mount /dev/sda3 on / type ext3 (rw,noatime,nodiratime,data=ordered) What's left as an option is to do it manually, guessing the related package by name and content of the file, which is usually straightforward.