best time to go is durin spring when the weather is not so hot and not so cold. if you like sightseeing, osaka and kyoto is recommended for the traditional feel (temples, geishas plus the cherry blossoms).
if you dig amusement parks, try Sir Galahad's suggestion of going to Disney resorts but I recommend the Universal Studios in Osaka since the rides are said pretty much like the one in the US. For extreme rides, Fuji-Q is famous. If you are planning to go to Yokohama, there's Sea paradise and go to Minato-Mirai 21 to check out the Cosmo Clock (Ferriswheel with bright lights and a digital clock in the middle).
Around summer, you can go to Ocean Dome. Never been there but looks expensive though.
Cost of entrance fees for amusement parks can cost around JPY3500-JPY10,000. If you are going to Universal Studios or Disneyland/sea I suggest you go there for 2 days to enjoy the rides. Queueing formajor rides can take as long as 3 hours esp. in USJ.
You have to try the hot springs or onsen if you are plannin to stay in ryokans. The cost for stayin in ryokans depends on the city you're stayin in. They rarely accept single travellers so it would be better if you go there by groups but they charge per person not per room. Average would be about JPY7000 per person per night. But still ryokans are cheaper compared to hotels. If you are goin wit a gf, then try at least to go to a rabu rabu hoteru (love hotel). Lotsa kinky stuffs (daw)...never been there so can't tell, but i've seen one online.
For transportation, JR is the most famous local train. They sell ride-all-you-can tickets for tourists. Try to google Japan Railways and check the ticket types. They don't sell that kind of ticket in Japan so I suggest to get it before you go here. It is easy to go around here cuz you can always check online which train you have to ride, what time you have to leave, and which trains you have to transfer to. Don't worry, if you think you got lost, you can always go back without payin extra. As long as you're still inside the train station.
As for food, you'll be overwhelmed wit the serving of the dishes. Durin summer if you wanna try Sobas or Udons, mind ya...they serve em cold. Must tries are ramen, sushi, yakuniku, kare, tempura. There are places that offer unlimited rice, eat-all-you-can, drink-all-you-can. Individual meals cost around JPY500-JPY2000. It's always nice to go to restaurants that have picture menus so you won't feel lost.
Whew and haba na pala..when it comes to Airlines I think China Airlines is the cheapest and when it comes to service I'd say you go for JAL.
Kung may tanong ka lang fireaway hehe.
Nice reply... Been to Japan countless times on account of my job... Tokyo (Nishi-shinjuku area) is where I usually stay for a couple of days beofer taking off to visit clients in Himeji, Yokohama, and Hamamatsu.
If staying for a couple of days... try getting a Rail Pass from JAL... This gives you all day and night free rides on the Bus, Metro, Subway, Express Trains and even the Shinkansen (bullet train). It's around 250USD for a 5 day pass but you can go crazy with it. It allowed me to see the japanese countryside while getting quickly to Kyoto, Hiroshima, Osaka, Nagoya and other cities within the validity period of the pass. The rail pass is worth it if you city-hop as just one roundtrip Tokyo - Kyoto Bullet train ticket would run up to 150USD or more. Heck, just the NaritaAirport to Tokyo express cost 60USD roundtrip.
If planning to only hit one city then the Rail Pass may not be an economical option. Tokyo in itself is a huge city and can take several days to explore it's hi-tech and cultural attractions. Akihabara is a must see and so is Ginza, Meiji Koen, ROPPONGI hills, and those who are for the daring Kabuki-cho in Shinjuko