I know the following Hondas are made in Japan:
-All hybrids (only Civic for now, but the new Insight & the 'sport hybrid' will be made there as well (Suzuka). All original Insights & Accord Hybrids were made in Japan (Accord was built in Saiyama). The Hybrids are largely hand-built, believe it or not.
-All S2000 (all years). Again, largely hand-built, since late 2003 in Suzuka - I forget the plant for the 2000-2003 run, and too lazy to go look it up at the moment).
-All Fit. (but probably not past this year - at least some of the cars will be US-built starting MY 2010, in either OH or IN). For now, all USDM Fits are sourced from Japan.
-A very few Accords (mainly EX trim with the 190HP L4). All V6 Accords are US-built, btw.
-A very few Civics (excluding hybrid, above) - mainly EX w/ 5-speed.
- A very few CR-V (mostly EX-L trim); some LX trims are made in Mexico (VIN starts with '3').
If you're looking for a J-VIN Honda, and it's not part of the 'exclusive' club, the best time is right after a model switchover - I think they do this to both help ramp up the production lines (not that it takes that long for Honda to switch them over), and to familiarize the JDM line workers with the new model.
As it turns out, all 3 of our Hondas are J-VIN cars - We have a Civic Hybrid, an S2000, and an EX-L CRV. We've owned US-built Hondas, too - and I think the better put-together ones have been the J-VINs.