There seem to be engine models still produced in Japan, and others that have moved to China. However I'm not clear on what overlap period exists when production is transferred. A Honda engine dealer can probably tell you which model is produced where, at least for the ones he stocks.
As a further complication, Honda has a range of reduced cost engines (the overhead cam, or OHC ones, which have a GC prefix for horizontal crankshaft or GCV prefix for vertical crankshaft). I haven't figured out where they are made. It seems to me they are clearly inferior to the pushrod ones, but they seem to be cheaper to make up for that.
Post Edit: Here is a list of plants where each model of Honda engine was built through 2010, with serial numbers, prefixes etc:
http://www.aapowerequipment.com/honda/2012_Honda_Model_Chronology.pdf
