I have a Sony STR-DA3100ES, which notes in the manual that can be operated by IR command, but the remote omits that command. I have searched, but have been unable to find it. Any ideas?

Can you be a bit more specific about the problem are you refering to using the 2nd and 3rd room zones or how you go about installing an external IR receiver or sender.
What page are you looking at

Background information about the zones & IR, as requested:
I have an IR connecting block in the main room. Connected to that unit's screw terminals (IR & GND) I have 14 AWG copper stranded wiring, which I connect to a BNC connection that heads out over quad-shilded RG-6 to the other room, on the other end, it's connected to the emitter output of a connecting block in that room. So, when I hit the receiver in the other room, the connecting block sends the signal out to the other connecting block, which emits to the IR port on the receiver.

Zone information
I have a 2nd & 3rd zone, but all the controlling equipment is in the main zone. As such, while there are 2nd & 3rd zone triggers, they don't assist me. I would like the components to power on when I turn the system on for the 2nd & 3rd zone. Currently, I have been unable to get the main trigger to activate unless the main zone is on. So, if I were able to send an IR command to activate the trigger, that would allow me to control that from the remote in the 2nd zone.

Manual information
Page 47 of the US manual reads as follows:
"CTRL: Lets you turn on or off the output of the 12V triggers manually by the CIS command of the IR remote or RS232C control."

i may be wrong here, but i beleive that this function can only be acheived using the rs232 control only. I will have a chack on there web site and possibly others will be able to assist

Yeah, I wondered the same, but it clearly notes IR as a possibility. We'll see.

After doing a bit of reading, i am of the beleif that it is a typo in the manual. I cant find any reference to it at [Link: hifi-remote.com] which lists most available IR commands. It is however referenced in the CIS RS232 protocol manual, there is a program here [Link: vibert.us] thats allows you to control your amp using the RS232 port.
There was some post over at agoraquest about the program.

have a read of the manual for the strda3200 on page99 there is a brief description on it there usinmg a remote, give that a try and let us know what happens