The biggest thing to consider when looking at EMS options are:
-Cost
-Install (PnP or custom hard wire?)
-Can you tune yourself? (otherwise you need find a tuner local to you)
-Does it work with your engine (most popular units work with everything, this mostly applies to rotaries)
-What features do you really need?
There are different types of EMS options as well, such as chip/reprogram/reflashing of the factory ECU
A piggyback unit that lets the factory ECU control most basic functions and the piggyback will control usually fueling and ignition (as well as other various features) at a preset point, usually when the engine enters boost.
A complete standalone replaces your entire factory ECU and gives you complete control over the engine, from idle to warm up characteristics to wide open throttle operation. These are more complex, usually harder to set and tune, more expensive, and sometimes have to be custom wired. And on newer OBD-II vehicles a lot of factory ECU's run the gauge cluster, ABS system, power steering system, even airbags and air conditioning systems. With a standalone you could loose all of this.
If you just need fuel/ignition control I would recommend a piggyback. Typically piggybacks aren't the best solution but for a good EMS upgrade you can't go wrong with one. The OEM ECU will control idle, warm up, and still run any accessories you may have.
For a piggyback I like the AEM Fuel/Ignition Controller (F/IC). It can tune with MAF (airflow meter) OR MAP (manifold pressure), has large tuning windows, is easy to tune with, and relatively easy to wire. The higher end version (F/IC 8) also has an expandable boost controller (you will need to buy the AEM boost control solenoid) built in so that's a HUGE plus and and a nice feature.
LINKThe HKS F-Con EMS is a great EMS but the system is locked from HKS so only an HKS Authorized tuner can alter the tune and even install the system. HKS does this to protect the reputation if you will of the EMS so people don't blame blown motors to this particular EMS. If you're not going to do any self tuning anyways then it isn't a huge deal and ensures you will get a solid tune, but adds cost.
Other good standalones are the AEM Universal EMS- it has a crap ton of features and honestly most people never use all of them.
The Haltech E8 is another solid standalone EMS that I really like. The software is awesome and easy to use, has great features, and a large support network of tuners. It reads all GM sensors too, which are accurate and easy to find and cheap, so it's easy to convert to wire it up. Plus, you can get used E8's all day for a good price. The Haltech E11v2 is basically an updated version of the E8 and has a lot more features and works really well.