Should we use the system cron, or a prefixed cron?

I'd be interested in hearing other's thoughts on this.  I guess on a
more general level, when should we rely on system
libraries/applications and when should we prefix?  I can see both
sides, if you install as a user, you want to be able to manage
everything yourself.  If you are running other services on the main
system, perhaps it is more convenient to have all the cron items in
one place.

Thoughts, ideas?

-matt
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