That sounds like it might be complicated to implement within Anuran, and at that point it starts to become an appointment minder, which I'm always going to try to respectfully argue against.
If you already use an appointment minder like EssentialPIM or Outlook these have the kind of popups you want, plus they can execute programs if you tell them to. If you don't have or want EPIM or Outlook, I use Pegtop PStart's launcher, which very reliably can automatically launch programs based on an hourly, daily, yearly schedule. It's good stuff and I recommend it every time I get a chance to.
So, where I'm going with this, if we program Anuran with the ability to launch the popup if Anuran is ever re-launched when it is already running, we can patch in this behavior without adding to the complexity of the software.
One benefit of this is that if you already have a schedule set into appointment software, there's no need to duplicate it within Anuran. Just add Anuran.exe as a program to run on the appointment.
Of course, if this is a fairly easy thing to implement, that's a different story.
As far as implementation goes, we could do worse than uTorrent's scheduler:
NANY 2010 Release: Anuran
Just substitute "Full speed" and "Limited" with "Popup Enabled" and "Popup Disabled."