Everyone talks up the Japan Rail Pass, and with good reason, it's great value and generally pretty easy to use. But there are some things you need to consider before you buy one, and there are times when travelling on the shinkansen isn't your best bet.
The passes are great value if you're travelling a lot during the alloted time. But if you're having to buy an extra seven days to fit in one extra train trip... it's not worth it. Going by shinkansen is definitely something you should do in Japan, but it's also a premium-priced experience, and there are good, cheaper alternatives.
Other rail passes
The JR Pass isn't the only game in town, there are a lot of other rail pass options which favour local trains. One cult favourite is the Seishun 18 Kippu which aims to promote 'a more leisurely approach to travel'. This means staying away from the Shinkansen. If you have the time (and aren't you on holiday?) this is a very cost-effective approach. The pass includes 5 tickets, which you can split between 5 people, or use yourself over the course of 5 days. Either way, it breaks down to a cost of only ¥2370 per day.
If you're sticking to a specific area it's worth finding out whether there's a pass that will work for you. For example, if you're visiting Nagano and Niigata, a 5 day JR East pass will give you great value.
Flying is surprisingly affordable and you'll find some passes to make it even cheaper. Japanese airports are also relatively hassle-free, so the prospect of an internal flight isn't as awful as it might seem elsewhere.
JAL offers the JAL Japan Explorer Pass, three fixed-price fares on specific routes for tourists visiting Japan. You could fly from Tokyo to Sapporo for ¥10800 or from Tokyo to Akita for ¥5400.
ANA offers the Experience Japan Fare with very similar pricing and route options.
Perhaps the cheapest option, don't be afraid to catch the bus! While it takes some extra time, the incredibly direct nature of the Japanese highway system means the journey won't be as onerous as you're imagining. A night bus will also save you on accommodation, and they are surprisingly comfortable.
A five day bus pass will run you ¥15000 and you have a two month period to use it in. You'll also find that buses head to places that trains don't, meaning you can get a little more intrepid in your travels.
Renting a car or a van
Pack your international driver's license (in Australia you can get one at the RACV, they only last for a year, the whole thing is kind of a rort) because you can't rent a car without one. You can collect rental cars at airports and train stations, and it's all a lot easier than you might think. Japan also has an incredible network of Michi-no-eki, or rest stops, where you'll find konbini, restaurants, bathrooms (showers!) and even places where you can park and nap.
Vans give you even more freedom to roam around, and are a great choice for areas like Hokkaido. While it might be more of a fine weather thing, they do come with heaters for winter van times.
Okay, so it's not the fastest way to get around but it might just be the most unorthodox! The Japan Ferry Pass costs ¥21000 yen and offers six trips during a 21 day period.
If you're on an overnight route, the pass will get you into a second-class berth, which is generally a private berth (think enclosed bunk) in a shared room. You can pay a fee to upgrade to a private room.