Some Tokyo Metro Tips...
The stations are designated by the "M" logo in white and blue that you see below
This is Omotesando Station - a popular spot in Tokyo for luxury shopping (and it's also a stone's throw away from Harajuku if you want to check that out too!)
You'll see what lines go through the station with the color-coded symbols on the signage
For instance, you'll see at Omotesando Station there is a yellow circle with a G and the number 02, a purple circle with the letter Z and the number 02, and a green circle with the letter C and the number 04.
All the metro lines and their color coding and stops can be found here.
This will help with planning out your itinerary and how to get from A to B. I particularly like the Ginza Line myself - it goes through a lot of great tourist spots such as Shibuya, Omotesando (a short walk from there to Harajuku), Ginza, Suehirocho (a 5 minute walk to Akihabara), Ueno and Asakusa. This can be handy if you aren't too confident with changing train lines and such - it is easy and user friendly once you get the hang of it, but I know when I first used the trains here I liked sticking to one train line until I felt comfortable branching out!
The Metro Stops have multiple exits
When in doubt, check the maps by the exits!
There are also maps by a lot of the exits so you can get your bearings. If for some reason the attraction you want to visit isn't listed with which exit to get out at, it can be as easy as looking it up on the accompanying map. Plus, it might even give you some inspiration for other cool spots to check out!
Most Stations have free Wi-Fi
Paper or Electronic Ticket?
If your balance is too low to cover the fare, the barriers won't let you through and it will make a sound to indicate that your card doesn't have enough cash on it. Don't fret - it's as simple as reloading it at one of the machines at the station. Again, they have English instructions too (just press the main menu button for English and you'll be golden!)
Buying a Pasmo card has an initial 500 yen deposit which you get returned if you hand your card back at the end of your trip - but I personally think they make a neat souvenir from your travels! There is more information about purchasing a Pasmo card on the Metro Site here.
If you'd prefer to just buy paper tickets, you can do that too - but you might be wondering how to calculate what the fare is from your starting point to your destination. Google Maps or Hyperdia are two resources that can help you out - pop in your starting and finishing points, and it will tell you both how long it takes to get there as well as the cost for your ticket so you'll know how much to pay.
Say for instance though that you didn't check the fare before you left, you can't read the Japanese signage, and you're concerned you won't know how much to pay to get from A to B. A way around this is to buy the lowest denomination fare on screen at the ticket machine - and when you reach your destination you can go to a fare adjustment machine (located before the exit turnstiles) to correct any amount that you might be short. It saves paying too much for a ticket if you're not sure.
Hopefully this helps as a small introduction in navigating the Tokyo Metro. It's clean, timely, and a great way to get around this wonderful city!