Hi bladerunner,
The oldest OS you can install on any Mac is the OS - and the build - it was shipped with from factory. So if your new Mac came with 10.6.5 somebuild, that is the earliest OS you can install to it. Anything older, even 10.6.5 generic-non-cpu-build will not install there.
I think part of the problem is that you were using migration assistant when skipping a release. Migration assistant is always tested as something to go to the next OS, so 10.5 -> 10.6, or 10.4 -> 10.6.
When you try to skip one release between there will be more differences than the migration assistant can detect. Also in the case of eMac to iMac intel, there is a completely different architecture.
If you had Mac OS X 10.5 retail disc set (black discs) available, you could install that on the eMac first, then use migration assistant again to get that 10.5 system's data migrated to that new iMac. If you don't have those discs, it won't be worth the price of getting those only for making the migration easier.
Before any migration it's good to make sure there is a good backup available, just in case.
You could import the items in the user's home folder manually to the new Mac's user's home folder. Some software would recognize their data needs to be upgraded to the newer version of the OS; usually at least Mail and Address Book do this easily. Also any bookmarks should transfer easily.
Most items should work or be upgraded easily by the system, but until everything is confirmed to be running and set up smoothly, better keep the backup safe.
But (even if the migration assistant worked when skipping from 10.4 to 10.6) you'll still need to install some programs from scratch. Some are newer than the older OS supported. Some are Intel- or PPC-specific so they will also have a newer version available.
Also any applications that intall any kext (kernel extensions) in the system in the install process will need to be reinstalled; migration assistant does not bring non-apple kexts to the new system.
