I think anyone running a megasquirt would qualify (CoyoteX figures prominently but there are some others using it):
megasquirt site:ecomodder.com - Google Search
* *MegaSquirt - Electronic Fuel Injection Computer by Bowling & Grippo * *
Kit Carlson designed/made his own ECU based on the atmega:
http://ecomodder.com/forum/showthrea...ment-5104.html
I'm not fluent in the commercial offerings though, but here is a google of ecomodder for "neptune"
neptune site:ecomodder.com - Google Search
I imagine there is some of this sort of thing going on in the xprize entries, zerofuel needed a custom controller IIRC, not sure if jpstaub (tdi/insight guy) did or not.
Might also consider people who are modifying sensor signals to trick the ecu into doing what they want, i.e. an efie (tweaks o2 sensor signal)
http://www.google.com/search?source=...&aq=f&oq=&aqi=
and/or faking out the IAT signal, etc...