Firstly, Quartz is more extensible. When you create the need for cron, quartz allready has support for this. The themes used by your application are also managed by quartz, so you do not need to start your own thread. It's nice that this is handled by a quartz planner. It also integrates with the spring framework (I don't know if this applies in your case). Quartz has reasonable documentation and is maintained by the community.
I do not know if java.util.Timer is really used in corporate environments, but it depends on your application.
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