Resources

GNU S12X/XGATE tool chain - The core tools required to build code for the MC9S12XDP512 chip we are using.
hcs12mem - Tool for memory manipulation of Freescale HC9S12 series MCUs through the Serial Monitor, BDM, or Serial LRAE interfaces.
Eclipse IDE - One of, if not the, best IDEs out there for all purposes, written in Java.
KICAD - A free OSS GPL schematic and PCB design suite for Linux, Windows and Mac OS X.

Octopart - Octopart is a search engine for electronic partsFormerly Radio Spares. This links to most of the good suppliers and is a very useful resource for pricing, availability and datasheets.
Technologial arts - Various Freescale-based educational and prototyping boards, including the infamous "TA card" that DIY oriented FreeEMS users base their ECUs on.
14 point 7 dot com - Several cheap DIY wideband controllers.
jbperf - Jean Bélanger's add-on board site, cheap versatile DIY signal conditioning circuits and more.

SDS EFI Tech FAQ - A good general EFI reference from Simple Digital Systems, manufacturers of low end, commercial, hand controller based EMSs.
MegaSquirt Manual - A fairly thorough (almost to the point of drowning the good information) EFI reference, specific to their hardware, but containing a large amount of good general information.
MS Extra Manuals - A good resource for information on integrating an EMS with your particular hardware.