Looking through this thread, I noticed a lot of people taking the bullet train between Tokyo and Osaka. IMO this isn't the best way to travel. It costs about 140,000 JPY and takes a couple hours.
I used to take the bus - 2000 yen for overnight, or 3500-5000 yen for daytime
Of course there are domestic flights. Most cheaper airlines fly from Narita, and cost about 5000 yen to Osaka. Budget airlines like Peach and Jetstar. Problem is, getting to Narita from central Tokyo adds a decent amount of time and price. Haneda is much closer to central Tokyo, where most people will be staying.
Three airlines have a route from Haneda. JAL,
ANA, and
StarFlyer. The benefit for tourists is that they all offer special rates for us. Forget JAL as their flat rate 100,000, while cheaper than bullet train, is still higher than ANA and StarFlyer. They cost about 7000 yen each for Haneda > Osaka.
IMO this is probably the best way to go. Although if you've never been on the Shinkansen, it is a tourist experience in itself. So maybe check that out once, or for one direction of the trip.
JR Pass is hardly worth it if Tokyo <> Osaka is your only main bullet train trip. If you are doing others, then this will have some benefit on top of the cost of the JR Pass. May still be more expensive than flying though, so be sure to compare. I've seen people directly answer "what is the best way to go from Tokyo to Osaka" with "bullet train" and IMO that's just bad advice if not qualified with other things like "if you want the train experience"