The MS1 ECU has been used successfully on everything from Ferrari's to 2CV's, 27 litre V12 Rolls Royce Merlin engines with 24 spark plugs to one cylinder lawnmower engines, so it has a proven track record. Indeed the MS2-Extra and MS3 ECUs can run all those too. The technical backup is not as readily available as an MS2, mainly because less people use it now, so everything has moved forwards to MS2, but theres still a forum for these on the MSExtra.com website. In most cases the MS1-Extra ECU isn't really worth the savings, because its only around £50 cheaper than an MS2 and the end results aren't as good. Tuning the MS1 is a bit cluncky, where as the MS2 is much more intuative and ends up as a much smoother setup. There are a whole host of features that the MS2 ECU has over the MS1 as well, especially as the MS3 code is being back ported to MS2, so its still very current. Where as the MS1 code has been left for a lot of years now.
The main advantage of the MS2-Extra ECU is that it can be used on a lot more vehicles without fitting a different crank wheel (e.g. Renault RENIX, Rover K series, etc). So the MS2-Extra is much more versatile if you want to go for a setup that's a more plug-n-play. It also has a faster processor and more RAM, so that allows it to be more accurate, e.g. timing resolution of 0.1deg with MS2-Extra, where as with MS1-Extra it is 0.3deg. The fueling control in MS2-Extra also has improved resolution, in theory it is capable of 0.67uSecs where as MS1 is 100uSecs. This means you can control large injectors better at idle with MS2-Extra. As you can see, MS1-Extra is still very impressive as far as accuracy is concerned, but MS2-Extra is clearly a step ahead in the resolution steaks. If your going to be boosting your engine and using HUGE injectors, then MS2 is the way to go, as it has better control over the fueling, in that the injectors can be controlled that much finer for better fuel adjustments, so idle and cruise speeds are easier to tune. Also having a 16x16 fuel table that the MS2-Extra code offers helps a lot when tuning a boosted engine! There are a whole host of features that the MS2 ECU has had back ported from the MS3 code, so its still very current. Now, the MS2 can also control 4 injector channels, so it can run a 4cy in full sequential fuel, as well as a 6 and 8cy in semi-sequential fuel.
This processor will give you all that the MS2-Extra code has, plus SD card datalogging (SD card slot is built into the ECU), USB comms (MS1 and MS2 need's a convertor that's costs around £35) and it can have another board plugged into it (MS3X) that will give it lots and lots of inputs and outputs as well as 8 injector drivers and 8 low powered ignition drivers. For more on the MS3X board see here. The MS3 also has a larger spark map than MS1 and MS2, 16 x 16 rather than 12 x 12. This ECU is the ultimate MegaSquirt!
This is pretty specific to your vehicle, in that if your application doesn't have one of the available plugs you can't use it. So if you have a plug that's suitable then you can take advantage of the DIYPnP ECU. It has a MicroSquirt module, running the MS2-Extra code, at the heart of it. With the ability to use 2 trigger inputs as standard, it can do sequential COP up to a 4cylinder, if you have the correct Cam and Crank signals. The DIYPnP also means you don't have to cut into your existing wiring loom to make it work. Most users will find that they will want to remove the AFM they're OEM used, this would mean some mods to the loom to add an air temperature sensor. This is not currently upgradeable to MS3, but there are MS3 versions of the PnP ECUs.
Most people find that an MS2 ECU is much smoother running than an MS1 as it has lots of better tools for acceleration enrichment and has a finer control over the injectors, I have to agree here, the MS1 is a fantastic ECU for the money, but the MS2 is a leap forwards and should be seen as the starting point. I also believe the MS2 is easier to tune than MS1, as the latest tuning software, Tuner Studio, has been written around it. Now there's also sequential fueling for MS2-Extra, semi-sequential for up to 12cy engines and fully sequential for up to 4cy engines, this allows the MS2 to compete against ECU's that are 5 to 10 times the price of an MS2-Extra. The MS2 has a trim table for fuel on each injector output (up to 4) allowing very high accuracy on most engines. Alternatively the MS3 has all the MS2, plus it has the ability to datalog straight to an SD card (built in slot) and it can communicate via the USB output without an adaptor. If you go for an MS3 with an MS3X board, it can control up to a V8 fully sequentially fuel/spark (COPs) and it has a trim table for every cylinder fuel and ignition up to 8 channels The MS3X will give you Launch, Switchable Maps, NOS outputs, spare ADC's, etc, so it's a case of weighing up if you need all those options for the cost.
So as you can see, there's no definitive answer as to which one you should choose really. All have their own merits, for the money the MS1-Extra ECU can't be beaten, it is simply the best ECU you can buy for the money, it out rivals many ECU's that cost several times as much, but then the same can be said for the MS2-Extra ECU. All the ECU's also have excellent technical manuals that I have helped to compile and a superb forum for help (www.msextra.com). The main thing to remember, is that all the MegaSquirt ECUs (except DIYPnP) can be upgraded to MS2 or MS3 if you feel the need, so even if you decide later that you wanted an MS2 rather than an MS1 or an MS3 rather than either of the others, then it can be modified at a small cost, and you have another model.