MegaManual
General MegaSquirt information including tuning and v2.2/v3.0 board assembly, etc. A great resource if you're building your own ECU, but not as useful if you're buying a pre-built one.
MSefi.com
A forum dedicated to MegaSquirt in its standard (B&G) form and running the standard (B&G) firmware. The discussions here are good for very general hardware troubleshooting and tuning advice.
MSextra.com
MegaSquirt information tailored to the MS/Extra firmware and corresponding hardware modifications. All MS3 MegaSquirt ECU's are running this firmware. Furthermore, all MegaSquirt ECU's for 420A/Neons's, whether MS1, MS2 or MS3, use the MS/Extra firmware.
MSextra.com Forums
MSextra.com forums.
MS1/Extra Documentation
Tuning guide for using the MS/Extra firmware with the MS1 processor.
MS1/Extra Firmware Packages
Download official MS1/Extra firmware packages here. At the time of this writing, 029y4 is the latest and probably final release.
MS2/Extra Documentation
Tuning guide for using the MS/Extra firmware with the MS2 processor.
MS2/Extra Release Firmware
MS2/Extra Beta Firmware
MS2/Extra Alpha Firmware
Download official release, beta, and alpha MS2/extra firmware packages here.
MS3 Documentation
Tuning guide for the MS3 processor. Much of the MS3 and MS2/extra firmware is the similar, so refer to the previous links for more detailed tuning information.
MS3 Release Firmware
MS3 Beta Firmware
MS3 Alpha Firmware
Download official MS3 firmware packages here.
If this list is confusing or overwhelming, first analyze your situation. If you purchased a pre-built and configured MegaSquirt EMS system determine which processor you have; MS1, MS2, or MS3. Ignore any of the links pertaining to assembly and hardware modification. For instance, if your ECU uses an MS2 processor, go straight to the MS2/Extra documentation. The tuning guide there is all you will need to begin.
If you have any questions specifically about the MS/Extra or MS3 firmware, post on the msextra.com forums first since the users there are the most knowledgeable about the MS/Extra firmware.