NO file in
~ has to be owned by root.
If a software requires that a file in your home directory be owned by another user, it is a bug and should be reported as such.
Other than that, a common case involves two security-related software that require restricted permissions on certain files, namely:
man ssh, section
This is the per-user configuration file. The file format and
configuration options are described in ssh_config(5). Because of
the potential for abuse, this file must have strict permissions:
read/write for the user, and not writable by others. It may be
group-writable provided that the group in question contains only
Contains the private key for authentication. These files contain
sensitive data and should be readable by the user but not acces‐
sible by others (read/write/execute). ssh will simply ignore a
private key file if it is accessible by others. It is possible
to specify a passphrase when generating the key which will be
used to encrypt the sensitive part of this file using 3DES.
Other files like
known_hosts, etc. should be writable only by the user, but can be world-readable.
~/.gnupg (and contents) should be accessible only by you. With other permissions, GPG will complain about unsafe permissions.