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. I think your best chance is to query the last access time by using stat and remove the files that haven't been accessed for a longer period. I suggest that you create a script that creates a list of candidates for removal, which you can check before finally deleting. For easy comparison by a script you can use the "seconds since epoch" format. And create a backup before changing anything.
$ stat -c "%x" /etc/wgetrc 2017-11-12 14:00:50.870671892 +0100 $ stat -c "%X" /etc/wgetrc 1510491650 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.