You can take a nightbus, there's Shinkansen, there's planes, and then local trains.
Nightbus is REALLY cheap. Nightbus between Tokyo & Osaka ranges from around ¥10,000 to ¥16,000 for a return ticket. The difference in price reflects the quality of the bus; the cheapest don't have toilets and are cramped. The more expensive buses are pretty nice, with reclining seats, slippers, etc. If you value your comfort at all, go with the more expensive one.
Shinkansen, unless you get a railpass through jtbusa is VERY expensive. However without a railpass, it can cost 16000yen upwards easily. Railpasses are only available for foreigners, and cost 300 for 7 days and I believe 500 for 14 days, and are good on all JR lines and shinkansen depending which type of pass you get. They are NOT good for subways though.
Shinkansen between Osaka and Tokyo is around ¥29,000 for a return ticket and takes about 3 hours. It costs slightly more to get a reserved seat, which I recommend if you are traveling with friends and want to sit together, or if you're as picky as I am about getting a window seat. ^-^
Local trains are very confusing, and it can take you 12 hours plus but I have crazy friends who've done it depending how far you go. We're considering taking the trains from Nagoya to Osaka for a day or two, because it's close and would cost us MAYBE 2000yen extra. But going from Osaka to Tokyo would take a long, long time, you'd have to transfer alot and it'd be crazily monotonous.
Planes are always an option and I'm not sure on price but I've talked to many japanese residents who fly. Sato flew from Ume to Tokyo and she said it cost her about 160, so average a flight from VA to FL, probably it's the same.
You can also fly, and this can be a good option if you are booking your trip way in advance and can get a good deal. Keep in mind though that this will not save you time over the Shinkansen because you have to take trains from the airport into both cities.
Shinkansen is really the most convenient way to get between the big cities of Japan, but bewarned - certain JR passes only cover certain regions, and sometimes it's hard to find a seat on a non-reserved car. I'd still recommend the Shinkansen over everything, though, if only for the experience of riding a Japanese bullet train. XD It's just cool!!