For AFP on anything but OS X, netatalk was missing a flush-to-disk command and failed the last time I surveyed.

Various samba versions have been implicated in backups that are corrupt when when you go to read them. There are enough people successfully using samba now for time capsule that I suspect that issue is a thing of the past or restricted to certain NAS devices.

Time Machine is a big enough bandwidth user that I presume we are talking LAN, and for many people their LAN is secure enough.