Exploring Tokyo solo for 3 days: Where to stay and what to do?

I would stay at Tokyu Stay Shibuya (Tokyo Stay Shibuya). It's a great shopping location and the rooms are great as well. Go to Tsukiji Fish Market (Tsukiji Fish Market), check out sumo, and Akihabara (Akihabara). Ganbatte!

Sawada sushi is mind blowing, you'll have to book w/ your hotel concierge, they are booked months in advance so call asap. 

Well, if you're trying to find Bill Murray the first place you should look is the New York Bar in the Park Hyatt Tokyo.

It's where Bill Murray and Scarlett Johannson's characters meet and the view of the city is beyond amazing. Just remember to have a whiskey in his honor!

Another pivotal location is the Karaoke Kan (it's where Bill Murray's character sings Elvis Costello) as is Ichikan, the sushi restaurant where they go to dinner. 

I would also check out Air, which is the nightclub they visit--I've never been there but I've heard it's a lot of fun!

If you'd like to experience the old Tokyo since 18th century, I recommend Yanaka, Nezu, Sendagi area called "YANESEN CENTER". JR Nippori Station or Ueno Station, Tokyo Metro Sendagi or Nezu station.

There are a lot of peacefiul temples, shinto shrines, little souvenir shops and cafes.

About Yanesen

Hotel

Ryokan Sawanoya http://www.sawanoya.com/eigo.html
Ryokan Katsutaro Tokyo http://www.katsutaro.com/index.html

Tokyo is AMAZING solo! I went in November and it was great. I stayed at the APA Hotel Ikebukuro-Eki-Kitaguchi and very much enjoyed exploring the Ikebukuroneighborhood. The hotel provided a map to local restaurants and had a very good breakfast. Ikebukuro Stationis very central and has all the important lines. I ate a lot of sushi at the local kaitensushi (conveyor belt) restaurant (I think it's called Tenkasushi). I also enjoyed visiting and shopping at Ikebukuro Tokyu Hands and playing with the cats at Nekobukuro, the cat cafe on the 8th floor.

I highly recommend visiting the Meiji Jingu Shrine and Yoyogi Park in Harajuku. I also very much enjoyed wandering around and shopping on Takeshita Street. There's a tasty gyoza restaurant called Harajuku Gyoza Lou within walking distance. 

In general, the Lonely Planet Tokyo Encounter guides (2012 and 2014 editions) are really helpful and full of good hidden gems, especially for finding good places to eat.

I found that paying for data on my smartphone and using Google Maps was super helpful, especially for finding my hotel at the end of a long day (bookmark it!). Have an amazing trip! 

I'll second what other have said and say that Akihabara, Tsukiji Fish Market and Shibuya are some must see places.

Tsukiji is best in the early morning, when all the shipments arrive. Arrive around 6:30 am to see the fish auctions and the real wholesale clients of the market doing business. I had sushi for breakfast around 7:30, after visiting and I swear it was moving, it was so fresh :D

Akihabara is best in the late afternoon/early-evening, which is when you'll be blinded by the lights and the movement. Make sure to walk into an Otaku store as well as explore some of the electronics megastores in the area.

Shibuya is for nightlife and high-end shopping, if you're into that sort of thing. I'd say beware of the small, labyrinth-like side streets: they get pretty sketchy pretty fast (learned that the hard way). It's still really safe, but if you don't want to end up face to face with a fishy sex shop next to a weird-looking club, stick to the main streets.

The other part of Tokyo that is great to walk around is the Tokyo Imperial Palace: it's a beautiful area with lots of sightseeing to do. I'd suggest buying a Bento Box at a restaurant or train station on your way there and have lunch around the Palace: plenty of places to sit down and enjoy the day.

Happy exploring!

My wife and I traveled there for two weeks for honeymoon. No tour guide no group. Studio Ghibli Museum is nice but the park around it is also very nice. Other than buying tickets at the Lawson stores, eating food from them is incredibly good too. Stock up on CC Lemon drinks from vending machines, something about them is perfect. The Tokyu Hands store is amazing as well and is near Shibuya Station. Floors and floors of shopping for so many souvenirs. And usually outside street vendors have nice deals as well. In Akihabara the game store Super Potato is a very cool trip.  

A bowl, or several, of gyudon from the restaurant chain Sukiya will give you a different outlook on Japanese food. It is more than sushi.

The The Peninsula Tokyo is amazing but quite pricey.  I usually stay with my former host family (20 years ago!).

For things to do, here are a few faves:

Studio Ghibli MuseumGhibli Museum: This is the real-life Alice in Wonderland. The most incredible museum I have ever visited, hidden in a park and designed by animation powerhouse Ghibli Studios, this gem is a homerun. Get tickets at a Lawson convenience store well in advance.

Tsukiji Fish MarketTsukiji Fish Market: Get up EARLY (around 5am) and see the largest fish market in the world. A single tuna for $40,000 USD? That’s low-end. Wrap up eating the best sushi in the world for breakfast in the outer market. Unforgettable.

Takeshita StreetTakeshita Doori: The kids and fashion here must be seen to be believed. Indescribable, especially sitting right next one of the most beautiful shrines in Tokyo. Red contacts and outfits that make Marilyn Manson look like Pokemon? Prepare to be amused.

Akihabara StationAkihabara: From “maid cafes” (you can sit in a mock living room and have maids at your beck-and-call for food, newspaper, coffee, etc.) to electronics years ahead of the US, this “computer city” is the mecca of geekdom. Otaku central. Moe moe kyuuuuu!

Have a blast!

Tim

I agree with the others who have recommended staying in Shibuya.  My favorite hotel there is Granbell Hotel Shibuya.  It's reasonably priced and very centrally located.  

Try Sensoji Temple,Shibuya 109,Akihabara and these are all in Tokyo. About a tea house,,um,,I like Kayaba Coffee（http://kayaba-coffee.com/info.html) You'd love it if you like Japanese nice and old-style houses!

3 days in Tokyo is going to fly by. Depending on the days you are there, it changes a little bit of what you can do. One thing that is constant is that the Yamonote train will connect you to pretty much everything in the city.

If you are going to be there over the weekend, the nightlife in Tokyo, especially in Shibuya and Shinjuku is solid. Be aware that the trains stop running around 12 a.m. and don't start again until 5:30 or 6 a.m. 

On Sunday's a great place to check out is Harajuku Station  its usually filled with people dressed in playful outfits and some of the latest edgy fashion in Tokyo.

If you are looking to do a little shopping I'd recommend Harajuku or Shibuya 109. 109 is Basically 8-9 floors of nothing but clothes, usually they have some pretty fashion forward stuff, the only downside is its right next to Shibuya Crossing and gets a lot of foot traffic.  If you're looking for something more glam then I'd head over to GinzaWish I could help with the Tea Houses, I'm sure someone else will have a good idea of where to go.

If you want to get out of the tourist areas, you could check out Akihabara to experience some Cosplay,Ekoda Station to get into a little more of a suburban area (I lived in this area for awhile), or Ikebukuro for some Fugu (blow fish), which I think is one of those experiences that you have to take advantage of while in Japan.

If you stay at Park Hyatt Tokyo, Meiji-Jingu Shrine is close. The historic shrine surrounded by forest is where I, as a local, strongly recommend you to visit. Visiting Meiji Jingu Shrine in the morning is even better since there are fewer people around and you may feel mysterious atmosphere.

Walking through Meiji-Jingu and Takeshita street, you would find a cafe called Omotesando Koffee.
Omotesando Koffee is in a japanese traditional house renovated for the cafe and gives an unique experience as you drink coffee in "Wa". The combination of espresso macchiato and baked custard is my favourite there.


Shinjuku Gyoen National Garden is also close to Park Hyatt Tokyo and nice place for brunch. The autumn foliage there is beautiful and romantic. Besides, there is a picnic ground surrounded by Japanese garden and I am sure it is nice to have take-out foods in that relaxing nature. For take-out foods, I recommend Delicatessen located at the 1st floor of Park Hyatt Tokyo.

At Rakuutei, a Japanese tea room in Shinjuku Gyoen, you can enjoy Japanese tea break in quiet and peaceful space.

Have a nice trip!

Keita

Depends what kind of stuff you are into. 

For example, if you are into gadgets and unique Japanese anime and manga culture, the Akihabara district is for you. 

For shrines and temples, you would probably want to try the Asakusa district. 

For museums, Ueno is probably your best bet. 

For odd Japanese fashion areas, you would want to go to Harajuku - especially on a Sunday. 

Park Hyatt where Bill Murray stayed in LIT, is located in Shinjuku. It's a huge shopping district and at night it has quite an extensive array of drinking and eating places.