P&K, its been a few years since I was there, but i still remember lots. Here's a quick brain dump.
I'll 2nd Akihabra - especially @ night!!
Visit the "departo's" (department stores) around Shibuya & Shinjuki for a look - the presentation is amazing (not to mention the price of some things eg beef). In Shibuya go to Tokyu Hands!!! This place has everything (almost) - wish there was one nearby here. Also checkout the 100yen shops, they're like $2 shops here, but masses better.
In Tokyo don't forget Harajiku on the weekend to checkout the "fashion" :blink: . Nearby, the Tokyo Bazaar (name ?) is a shop with good souveniers. Asuksa (sp?) is an easy intro to Japanese temples, & tourist oriented shopping. The neaby suburb of Kapabashi (sp?) is the restaraunt supplies district - great for knives, plastic food etc. Get up real early & go to the fish markets for the auction of the tuna. You'll get some great photos there walking through the stalls.
Stay in a love hotel if you dare - you'll recognise em when you see em ;-) You can rent a room for a "rest" (a couple of hours, or a stay (overnight). Rates are cheaper after 11pm :super:
Niko, about 2 -3 hours north of Tokyo has some amazing temples including the original 3 wise monkeys (400 + years old) but could be missed especially if you go to Kyoto.
Kyoto is a must. If it is still there, stay @ the backpackers near the Kinki Nippon Railway station - it was the best place I stayed at the whole time I was in Japan (not the flashest, but good company & an interesting host who got the whole place pissed 1 night :beer

. You can hire bikes there cheap & ride around all the sites as the city is pretty flat. (Avoid the YHA on to the north - very strict eg lights out @ 10!!) The golden temple, Nanzenji & Tokadai are all incredible, but so is the residence with the "nightingale floors". (you'll probably be templed out after Kyoto). Go down Gion early evening / night for some Geish spotting. Visit teapot alley.
You must go to a suburban "Onsen" (bathhouse)!! There is one around the corner from the Kyoto backpackers. They are fabulous - especially after a day of riding around! Look for the chimney.
To the east of Mt Fuji is the Hakone region with pretty lakes, great views of Mt Fuji & beautiful woodwork (bring back some bowls, coasters & puzzle boxes for top souveniers/presents). Sorry i can't remember the names of the towns.
Hiroshima should be on everyones list of places to visit I reckon. I found to be an incredibly moving place but also one which shows mans ability to move on whilst not forgetting the past. It is well worth the visit (find the epicentre; go to the museum; wander through the gardens; see Sudako & all the paper cranes; ring the peace bell).
Not far from Hiroshima are 2 places I'd also recommend. 1 is Miyajima & the Itsukushima Shrine - where the Tori gate to the temple is in the water (its that famous Japanese tousist promotion shot). The other is Iwakuni, a town where the samauri lived on one side of the river & commoners on the other. There is an amazing humped bridge between the 2 sides.
Himeji castle (about halfway between Kyoto & Hiroshima) is one of the few original castles left - I loved it. you really got to understand the whole fuedal system there.
Other suggestions:
- Don't forget if the timetable says the train will leave @ 7:04 it does - don't be late.
- Eat the "Seto" (set meal at lunch & grap a few yakatori's in a bar in the evening with a few beers.
- beer/spirits are available from vending machines on the streets.
- Don't get lost in one of the 17 exits to Shinjuku station! or you will end up blocks & blocks away from where you want to be
- If the train ticket machine isn't in english just buy the cheapest ticket as there are "fare adjustment" machines at the exits of all stations
- get english maps from the japanese tourist centre here before you go
- get a lonely planet guidebook!!!!
- I got a JR pass when I got there (from the JR centre which was @ either Shibuya or Shinjuku I can't remember). It was great as I had my Shinkansen (bullet train) tickets all booked & ready whenever I had to move on - no queueing for tickets or language issues.
Have a great trip
Crozdog