Back at Tokyo Narita right now, so figured I'd post my experiences.

It looks like Hertz is tied up with Toyota Rent-A-Car in Japan, so many locations will be Toyota RAC branches (at least at local branches, not sure if the airport locations are the same way). As such, the cars are all Toyota models as well -- the standard class being a Corolla/Prius and midsize being a Premio/Allion/Caldina (the former two are sedans, the latter is a rakish-looking wagon). The next class up is the Camry and Mark X (which I reserved). You can also reserve the Crown (Japan only), Windom (Lexus ES330) and Celsior (Lexus LS430) under their "prestige" classes.

Making a last-minute reservation is somewhat difficult though, as there is a 36-hour advance notice for a specific car/class, since it has to be processed through TRAC. Because mine was only 24 hours in advance, I ended up booking directly through TRAC instead.

In addition, I also rented a RX-8 through Mazda Rent-A-Car in Hiroshima, which was the perfect ride to pull up in for a factory tour of Mazda HQ.