Personally, I prefer a per-user crontab. For one, it's the only thing a
plain user can modify directly if he or she wants to manage jobs. In
addition, I believe it's the only mechanism that works consistently on
all modern UNIXen. However, the /etc/cron.*/ stuff is useful for
packaged software.
I think the per user crontabs should be avoided. It's much less clear and obvious than the crons in /etc. I find it's easier to version control them, as people need to have root/sudo access to update them. I'm sure we've all had instances where critical crontabs stop running after an account is disabled when an employee leaves.