Haven't seen this question before, so
 

If I go with something like an AEM or PowerFC, does that disable the OBDII port at all? I'm going to get a DashDaq with the Zeitronix Wideband, and I don't want it to become useless when/if I go with a full stand alone.

Zeitronix DashDAQ reads all Zt-2 data, so OBDII connection is optional. It's basically a top of the line Zeitronix display with logging and GPS capabilities

I appreciate the response, but I knew all that :-) my question is will it still be able to read engine parameters through the OBDII port even if I'm using an aftermarket ECU such as the AEM.

As a side note, I can't wait until I order my dashdaq/zt-2 with nav, it looks amazing compared to my old dashhawk!

No. There is no OBD system for AEM. Furthermore, there is no reason to go standalone these days with advancements in the stock ECU.

AEM does not output any OBDII signals.

Thanks!