I get notifications, mostly email, through the night. Most of them are commercial emails that go out at 2-4am and wake me up. Is there a way, or an app, that allows the notifications for alerts (not phone) to be automatically shut off for specified hours?

What phone do you have, my thunderbolt allows me to set 2 different download schedules, one for peak hours and one for non-peak.
If you have that option, first define your peak hours and then set your non-peak to download manually.
With that set up you should only get mail at night if you want it.

HTC EVO 4G. I may have found an app called Timeriffic that might do this. Downloading now.
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Timeriffic will do exactly what you want. You could also look into using the Priority Inbox within the Gmail app.

Got Timeriffic. Looks like exactly what I'm after. We'll find out tonight!

Thanks for the help.

I use Locale. Have a "sleep" profile that automatically triggers based on time of day, and silences notifications (and even turns off data to save battery).

Adjust "Time of day" for notifications

I have an ap that came on my phone titled "Smart Actions" that lets me adjust the time of day that notifications will sound a notification. Check it out.