Don't use rules to try to take the thinking out of the fundamental thinking process!
I only use e-mail rules and alerts to either automatically trash e-mails that I know I will never want to see or read (e.g. regular mass-mails that don't pertain to me) or e-mail alerts (e.g. automated e-mails from monitoring tools that may indicate a serious problem with an application that I support).
I do not use e-mail rules to file e-mails for me automatically. Doing so mixes stuff that I've not processed yet into my action and reference folders. I need to trust that my inbox is the only place that I have unprocessed stuff or I'll go numb to the whole system and won't trust it.
The only exception to that rule is filing sent messages with *wf* in the body to my @Waiting For folder (a D.A. Outlook trick).