Hemitronix vs Megasquirt $

Part of it depends on what features you're really looking for. You can do a batch fire MS setup cheaper than a sequential for instance. Also, the standard speed density style system of the MS is likely cheaper than the cost of a mass air flow system as those sensor tend to be fairly expensive, though it requires retuning the engine after mods. The mass air flow system tends to compensate for mods automatically to a degree.

Looking over what was required on the Hemitronix system, you wouldn't need to mess with the reluctor rings with a MS, could use all the standard Hemi sensors (assuming you get them with your engine to begin with), and can keep the factory coils. Here's a plug and play MS setup for the Hemi that's pretty capable http://www.efisource.com/shop/ms3-gen3-hemi-plug-play-gold-box/. You'd still need a throttle body, fuel pump, regulator, and O2 sensor(s) with this one, but it would use all the factory sensors and coils.

What specific features are you looking for? That might help to eliminate some of the options better.