It is possible to do may modifications to the hardware of a Stock ECU.

You can convert Auto To Manual.

You can convert One Wire To4 Wire O2 Sensor if starting with a P08 or P05 ECU, for instance. (OBD1)

You can Get rid of Cruise Control/Upshift Light after converting a P05.-- sonictronic - 23 Feb 2006

You can convert ECUs Non Vtec-To-Vtec. (OBD1)

You can Add IABTo P28 so that it can open the IABs on a GSR or H22 dual runner manifold. (OBD1)

You can mod you o2 input for 0-5v .O2 Input Mod -- CJ - 24-0kt-2005

You can Add Knock To P30 G00 -- CJ - 24-0kt-2005 -- Warning about adding a knock sensor

You can add a Knock Sensor to a p75 to complete the p75->p72 conversion (OBD1) -- Darksmiles - 19 Feb 2004 -- Warning about adding a knock sensor

You can Remove a Knock Sensor from a P13

How To Log External Data Such As An Egt Sensor (OBD1) -- markolson - 24 Oct 2005

You can modify Hardware For One Wire Vtec (OBD0)

You can disable Electrical Load Detector in a PM6, allowing you to use it in a car that dont have an external ELD. The Canadian PM6s are identical to the US PM6s except they lack ELDs, so look at the differences between Canadian and US ECUs (OBD0)

90 and 91 PR4 integra ECUs come in two varieties, aside from auto and manual. Some have an internal PA sensor, some have an external PA sensor. It is rather trivial to Adjust PR4 Pa Sensor

Parts For ECUs is a fairly comprehensive list of the parts needed for ECUs.