Resources: http://www.japan-guide.com/e/e2164.html
http://www.tourism.metro.tokyo.jp/english/

Tokyo is generally a good introduction to Japan, but it is not all that Japan can offer :)
It's mainly a metropolitan city good for shopping, dining and a little culture on the side.

What's the local transport like?
Generally, you can get anywhere you need to go via the complex but comprehensive train system.
You can divide them accordingly to the following categories:
1) Railway lines owned by Japan Railway (or JR in short)
2) Tokyo Subway Lines
3) Toei Subway Lines
4) Private Railway companies

Tokyo is one of the few cities where JR lines pretty much brings you anywhere and everywhere in the city. It's pretty much catered for tourists, making it easy to travel around mostly on the JR local lines.
I find that the subway lines tend to cater more for locals, stopping at more residential areas.
But subway lines can offer good shortcuts and access to places without any JR stations such as Asakusa and Tsukiji.

The main JR line that any tourist in Tokyo would take is the JR Yamanote line.

You can find the JR route map here http://www.jreast.co.jp/e/info/map_a4ol.pdf
And the subway route map here http://www.tokyometro.jp/global/en/service/pdf/routemap_en.pdf

Private railway lines tend to lead to the outer parts of Tokyo and to other prefectures or cities.

Should I get a pass?
I get this question very very frequently.

In regards to the JR Japan-wide pass:
If you are travelling just to Tokyo and probably doing day trips to close-by areas, No.
If you have an open jaw ticket and planning to take the shinkansen for a long haul trip once, No.
If you are planning to take a long haul trip on the shinkansen at least twice, maybe.
Why maybe? Go read my JR pass section :)

In regards to the passes offered by Tokyo Metro or Toei Subway:
This is a little complicated.
I would say no. why?

Before I start, I tend to keep to 2 major areas in a day in my sightseeing plans. Which is also probably why i don't pay as much as the passes are worth.
So my views are based on what I feel it's the best for me. Your itinerary might be different, especially if you like to travel to many places in a short a time as possible.

Lets take the example of the Tokyo Metro pass.
It's 600yen for 1 day and 980yen for 2 days
I generally feel it's not as easy to get around using only Tokyo Metro subway lines (means NO Toei subway lines as well!), you either use JR or it's a mix.
And it's hard to chalk up enough rides to justify the cost, but then again I'm a slow sightsee-er.
As i always advise, calculate your actual costs before you commit to a pass.
Sometimes it's better to pay as you go. I personally like flexibility in travelling routes.
BUT.... the tie-in offers with the Keisei trains and Airport limousines make it a very attractive offer. I'll explain in detail later.

There is also the Tokyo Metro and Toei One-day Economy pass that costs 1000yen.
Unless you are really rushing around and trying to soak up the entire of Tokyo in 1 day. It's a hard to chalk up 1000yen. BUT, if you can actually spend more than 1000yen in 1 day on the subway.. by all means :)

What about the Suica?
I love the Suica.
It's convenient, accepted on JR lines, Tokyo Metro and Toei subway lines.
You can always easily top it up at any JR station, and the amount balanced is refundable.
PLUS.... you can use it for purchases!

Only thing about the Suica is that it DOES NOT have any discounts on travel.
*there is the Suica-N'ex package thing... click on link to read further
It comes at a great deal in the Suica-N'ex package, which i highly recommend getting.

do read my Suica post for more info http://nexasjapan.blogspot.com/2008/10/suica-and-suica-nex-package.html


To round off...
for all train changing and train costs and details... Use this website http://www.hyperdia.com/
Will also dedicate a post on that. Look out for it!