Are you going to Japan? Here's some some of the advice I've sent to friends and family over the last few years...
High Level Strategy
Part of the wonder of Japan is the juxtaposition of massive metropolis and remote, magical, forested mountains. You can hop on a train and follow that gradient from one extreme to the other in less than an hour or two. It's quite nice.

A good first visit will give you a sense of each. It might look like:
• megacity Tokyo—2-4 days
• take the bullet train (shinkansen) to Kyoto
• former capital Kyoto, with many day trip options—3-6 days
• take the shinkansen + regular rail + maybe even bus to a remote mountain town
• relax in a traditional inn (ryokan) while soaking in hot springs (onsen)—2–3 days
• get back to Tokyo
• megacity Tokyo (remember how crazy it is), maybe plan for final night reservation at a killer omakase sushi restaurant before you fly off outta there—0-2 days
• go home and think about all the other cities in Japan you should have visited
General Note[s]
• If you will travel much by train, order a JR Pass ahead of time. It will pay for itself if you ride the bullet train. Get your voucher ahead of time (jrpass.com / japanrailpass.net / etc.), exchange it when you arrive at the airport, and flash it to get through any manned gate in a JR station.
• US people won't need a power adapter, but their 2-pronged plugs aren't grounded, so no 3-prongers.
• If you stay in an Airbnb, breakfast may be a tricky situation. Breakfast is generally the "family meal" in Japan, and diners or American-style breakfast places are few and far between. You'll get the traditional breakfast if you choose in a ryokan, but consider a grocery store and breakfast in-house, otherwise...
• 7-11 has everything you need. The food options are fresh, reasonable (did you forget about breakfast?), always available, and convenient. Even in weirdly remote towns they make a tasty fried-rice onigiri for 130 yen. You can use their ATMs to get your JPY with a standard debit card. You can copy and print things, and buy all of the personal stuff you forgot to pack.
• Yen are like pennies. Just move the decimal 2 places to the left and you'll have a reasonable rough-conversion of price (but the dollar/euro are actually a bit stronger.)
• Whatever you do, please find time to spend in an onsen. Guys will get a lot of Japanese man-dong and girls will encounter Japanese ladyparts but there is no shame here—everyone just wants to soak in relaxing hotspring water like you do. Take a quick etiquette refresher before you go!
Tokyo
It is a rad city. The trains go everywhere, they're are amazing once you catch the hang of it. The signage & transfer indicators are thorough. You can get almost anywhere in 30–40 minutes; 15–20 minutes of train time and a bit of walking on either end. Vending machines abound—you'll never need to go without green tea, or milk tea, or hot canned coffee, or corn soup, or... you get the idea.

I recommend having a day to wander aimlessly (or with at most 1-2 distant destinations): try and get a bit lost, pop into cafes and restaurants and find out what happens. Museums and exhibitions are a very good idea, too.

Dave favorites:
• Find your way to 21_21 DESIGN SIGHT.
• See the Daikonyama T Site.
• There is a nice little paper store in Harajuku.
• Maybe a reservation at Le Ginglet? The wine is A+.

Some general things/areas recommended from my brother:
Shinjuku: there is the Golden Gai district, it's a few hundred bars crammed into a square mile, some with 100 bars, some as small as 2 seats, and great ramen.The government building is cool, you can go to the top (45th floor!) for free and get a full view of Tokyo. There is a really nice tempura place there too. They have some of the best I have eaten in Japan.
Shibuya: you can see the scramble there, the world's busiest crosswalk. There are some interesting bars in there area too, or clubs if you are into that.
Harajuku: if you enjoy people watching and interesting shops, Takesitadori is a good area to go to. I would recommend going more on the weekend. You can pop over to Yoyogi park and see Meiji Jingu shrine... and the Japanese Grease guys. It is a really interesting sight to see. There is also a good cheap Gyoza place, and a craft beer bar around there too.
• Watch Sumo, I haven't actually done this yet, but it's something I really want to see in person one time.  I never really knew how intense it was until I saw it on TV here.  Tournaments are held every so often, so it might depend on when you are coming here. Check in advance!
Kyoto
What a place! Many day trips! Osaka & Nara are in near reach. The Gion-Shijo district is beautiful, full of people, has many nice meandering alleys, and there's a great big river you can walk and sit and drink along.

All of the tourist stuff is actually pretty awesome: Fushimi Inari (vermilion gates), Kinkaku-ji (golden pavillion), Arashiyama (bamboo forest), and so on. So good.

Here are a couple other more mundane (food/beverage oriented) waypoints:
Suntory Yamazaki Distillery—it's not too far and you can get a tour + drink from their whisky library... amazing! Look for a reservation ahead of time!
Len near Gion-Shijo—hipster coffee + traveller hostel, in case you need some English, directions, or a delightful pour-over
% Arabica—one near Arashiyama: successfully found delicious coffee here in November 2017
Kazu's Bar—rocking speakeasy-type-spot, find Elephant Coffee, in an alley off an alley, after 11pm walk to the 3rd floor and look for a door handle wrapped in duct tape... 3 years of great times here, the later you're there the better, and if you can find some Tantakatan (shiso shochu), get a cup neat
Musashi—get your conveyor belt sushi on. The price is right and you can eat a lot. Horse, if you want it. Many great options. Go in off-hours if you don't wanna wait.
Other Destinations & Onsen Towns
I've had great luck booking traditional ryokan with onsen through booking.com or hotels.com. There are other especially fancy and out-of-the-way places you won't find on there... but these work well for tourists. Shell out for the half board (breakfast, dinner) to get traditional food, and make sure to wear your yukata everywhere. Note: The further you go from a big city, your experience will be less English-speaking (and more interesting / confusing).

Here are some places I recommend and direct recs from my brother in quotes. 
• Fujikawaguchiko, a nice onsen town at the foot of Mt. Fuji with good hikes, beautiful lake[s], the suicide forest, and many other things to keep you occupied for a couple days.
• Kusatsu, a smaller and further out town with many hot springs, volcano hikes, and a wide range of traditional hotels.
• "Nikko, it's like the Lake Tahoe of Japan, there are great hikes up here, and a nice lake."
• "Hakone, if you want to go to some Japanese hot springs Hakone is famous for them."
• "Kamakura, it has some really nice temples and areas to hike, if you're into that thing." — There is also a giant copper buddha statue to see, and make sure to stop at a wonderful coffee shop called "The Good Goodies" for a delicious pour-over.
• "Odawara, it can be a nice day trip from Tokyo.  There is a castle to see and it's near the sea, so it's a nice place to visit." It's an OG sengoku jidai samurai castle, man!
• "Nara, I have heard Kasuga-taisha is really cool. There are deer roaming around freely in a park around the temple, they are really used to people too and will walk up to you."
Key Foods Checklist
• Ramen: it's noodles and broth
• Udon: it's bigger noodles and broth
• Soba: it's buckwheat noodles... and broth; try cold and hot
• Sushi: go big for at least one omakase meal, don't sleep on Kaiten Zushi either
• Takoyaki: octopus balls
• Curry rice: Japanese curry is is mild, rich, slightly sweet
• Mochi: if you can find ichigo daifuku you're in for a treat
• Tempura: they know how to fry out there
• Taiyaki: a fish full o' beans
Omurice, maybe, if you read this article
• (Sake, of course, and there's a strong natural wine game in Tokyo & Kyoto)

Bonus Items
The Japanese Tradition, Sushi—don't believe everything you hear
Hamidashimono—a fancy little gift set via Studio D collaborators
• If you see my brother, he might show you to a  nice meal, a special sake spot, or a secret stand-up sushi counter. Give him a high five for me.