running the MSD 6-Hemi ?

The Megasquirt can be set up to run the spark, but you'll need ignitors to drive the coils if you run with the new Hemi. Megasquirt has their own setup now based on some Bosch ignitors that were commonly being used to do such a thing (http://www.diyautotune.com/catalog/quadspark-four-channel-ignition-module-p-481.html). I think the FAST system is the same way, they have a separate box to run the ignition (FAST XFI for fuel and XIM for ignition). Not sure about the AEM, I know some of their boxes have built in drivers (the one I worked with did, but it was the universal EMS), but I can't vouch for what exactly the Mopar brand one has for features.

There are several members here with experience or plans for a Megasquirt build and I think there's one or two people planning for the FAST system. For a pretty wild build using a Megasquirt you might check out MadDart's ridiculous twin turbo small block setup over in the forced induction forum (Twin Turbo 67 Dart Project). Gives you an idea just what all a home made engine computer can handle. Don't think I've ever head of anyone popping for the Mopar AEM computer around here yet.