The reason for these being created with root ownership in the first place is usually the way sudo preserves some user environment.
ls: cannot access .gvfs: Permission denied

That folder .dbus and .cache with all it contents is supposed to be owned by the user whom the home directory belongs to.
It is usually safe to delete either, it will be recreated next time you login (it is just a cache that would have gone obsolete eventually).

# be careful what you type when you use rm -rf!

sudo rm -rf ~/.dbus

Keep in mind that .gvfs behaves somewhat special since it's a mount point (check the output of mount to confirm). As long as you have network folders mounted, don't touch it.