First a few definitions:
1) Central Tokyo
Usually defined as either the 23 wards (here's a list of the wards and a map of where they are) or the smaller area surrounded by the Yamanote railway line (about which more later), both of which are centered on the Imperial Palace.
I'll mainly be focusing on central Tokyo, for the simple reason that a short-term visitor to Tokyo is almost certain to spend most of his/her time within this area.
2) Greater Tokyo
The official Tokyo metropolitan area, which extends quite a way to the west (see this map - it extends from the left side to the right, covering an area a third of the way from the top to a third of the way from the bottom).
3) Tokyo as an urban area
This covers a far wider area, and if you're not too strict with your definition, could be considered to extend beyond Yokohama to the south, into Chiba Prefecture to the east and across the southern part of Saitama Prefecture to the north.
There's three forms of transport generally available within Tokyo:
1) Taxis
Expensive (650-660 yen to get in and go less than 2km, worse late at night - a trip across central Tokyo could easily cost 5000-6000 yen) and only really useful if you can speak Japanese or if you're going to a well-known location (or if you're lucky and strike the odd English-speaking driver). The easiest choice if you're confident you can explain where you want to go, and don't mind coughing up for it.
2) Public buses
Relatively cheap, but more common in the suburbs than in central Tokyo, and you probably have to be familiar with the bus route, understand the announcements in the bus about the next stop, know whether (and how much) to pay when getting on or getting off... not really worth the trouble unless you're travelling the same route several times repeatedly.
3) Trains
This is what I'll be talking about, for the simple reason that I haven't seen anywhere to match Tokyo's railway system for sheer convenience (and that includes New York and London); in addition, the railway stations mark pretty much everything in English, making it easy for even the first-time visitor to find their way around without too many problems.
There are three major types of railway available in Tokyo:
A) JR
The initials of Japan Rail, the privatised form of the old JNR (Japan National Railways). More precisely, JR East, which covers most of the eastern half of Japan, including the Tokyo area. Generally cheaper than the other lines. Transfer between interconnecting lines is generally free, as long as your ticket covers the end-to-end cost of the trip (and there's a lot of JR lines - here's a PDF map of the lines covering the greater Tokyo area).
B) Tokyo Metro
A group formed of multiple private railway companies that interconnect within Tokyo. To give you an idea of the scale of the Tokyo Metro railway system, here's a Japanese map for central Tokyo. (Here's an English version of the same map, in PDF format.) Note that these maps also include the Toei Subway lines described next.
C) Toei Subway
A group of four subway lines run by the Tokyo Metropolitan Government. Includes one of the newest lines in Tokyo, the Oedo Line (see below).
To begin with, let's take a look at the main railway lines within central Tokyo.
1) Yamanote Line (JR)
A ring line that goes through a large portion of the major statiosn in Tokyo, including the five busiest - Shinjuku, Shibuya, Ikebukuro, Tokyo and Shinagawa. Shown as "Yamanote Line" on the JR map above and marked in green. (These colours generally used to correspond to the colors of the train carriages running on that line, but newer carriage models just have a single or double coloured stripe instead of being painted that colour all over.)
2) Chuo Line (JR)
Runs on a east-west path across the middle of Tokyo - if the Yamanote line is an O shape, the Chuo line would change it into a theta. One end of the line is at Tokyo Station, and it passes through Shinjuku on its way out to the far western reaches of greater Tokyo. An express line, so it doesn't stop at all the stations it runs through. Shown as "Chuo Line [Rapid Service]" on the JR map above and marked in orange-red.
3) Sobu line (JR)
The slower equivalent to the Chuo line in that it (mostly) runs parallel with it across central Tokyo. Used to get to the stations that the Chuo line doesn't stop at, although the Sobu line doesn't go to Tokyo Station, instead bending upward to stop at Akihabara before heading out into Chiba Prefecture to the east of Tokyo. Shown as "Chuo Line Sobu Line [Local Train]" on the JR map above and marked in yellow.
4) Marunouchi Line (Metro)
One of the oldest subway lines in Tokyo, it runs in a half-circle through central Tokyo. Shown as "Marunouchi Line" on the Metro map above and marked in red.
5) Hibiya Line (Metro)
Runs from northeastern central Tokyo around the eastern side and down to the southwest edge, finishing at Nakameguro Station, one stop past Ebisu Station on the Yamanote Line. Shown as "Hibiya Line" on the Metro map above and marked in grey.
6) Oedo Line (Toei)
One of the newest lines in Tokyo, it opened five years ago with the intention of providing a ring line through parts of central Tokyo while connecting with a large number of other lines. To be honest, I've never really found it useful (with a couple of exceptions), but it's nice and new and goes to some places that can be hard to reach otherwise. Shown as "Oedo Line" on the Metro map above and marked in a pinkish colour.
7) Ginza Line (Metro)
I believe this is the single oldest subway line in Japan - useful mainly because it doesn't have as many stops as, say, the Marunouchi Line, and thus can get you where you want to go faster than some of the other lines, although most of the stations it runs through are accessible by other means. Shown as "Ginza Line" on the Metro map above and marked in orange.
Obviously, railway lines aren't much use unless you have somewhere to go, so here's some brief descriptions of the major railway stations around central Tokyo and what they have to offer.
A) Tokyo
Smack in the middle of a large office district (the Yaesu/Marunouchi area), there's not much in the way of entertainment here for the average tourist - with the exception of the Imperial Palace. Go out through the Marunouchi side, walk straight along the wide avenue leading away from the station, and you'll hit the edge of the Palace in a couple of minutes. There's not actually that much to do at the Palace - unlike Buckingham, there's no large building open to public view, although there are some nice gardens in the interior (entry's only allowed Tuesday-Thursday, I believe) and some not-so-nice gardens and traditional gates around the edges. Accessible on the Chuo, Yamanote and Marunouchi lines, as well as many others (including the Narita Express, which comes in from Narita International Airport, and many of the Shinkansen lines, the so-called "bullet train").
B) Ueno
This station has traditionally served as the final stop for lines coming south from northeastern Japan. Among other attractions, there's Ueno Park (which, by the way, looks like this during cherry blossom season), home to several national and metropolitan museums and art galleries. Next door is Ueno Zoo, mainly famous for its pandas. Accessible on the Yamanote, Hibiya and Ginza lines, among others.
C) Shinjuku
The largest station in Japan in terms of the number of people who pass through it every day (several million), the area around it shows two things: (1) you really can build lots of tall buildings in a country famous for its earthquakes if you really want to, and (2) no matter how hard you try, it's really hard to get rid of the grottier sides of life. Shinjuku has probably the largest group of highrise buildings in Japan, as well as one of Japan's largest red-light districts - the infamous Kabukicho, full of cheap and dirty watering holes, "pink salons", view-by-the-minute video booths, gay bars, gangsters (of both the Japanese and Chinese variety) and girls. Accessible by the Yamanote, Chuo, Sobu, Oedo and Marunouchi lines, as well as some Shinkansen lines, the Toei Shinjuku Line, Kawagoe Line and others.
D) Shibuya
A big shopping district, you might feel a bit out of place here if you're over 25 (or maybe even 20) - the Shibuya crowd tends to be young, fashionable and jaded. The area includes many too-trendy-for-you boutiques, a bunch of love hotels, and a few department stores. Accessible by the Yamanote and Ginza lines, plus others.
E) Roppongi
A much smaller station than any of those above, it's mentioned because it's popular among a certain section of the foreign population of Tokyo as the place to go for nighttime entertainment. Full of... er... non-traditional drinking establishments, it might suit you if you enjoy clubbing. Has become slightly more upmarket since the very large Roppongi Hills office/apartment complex (the buildings in the bottom left quarter of the linked map) was finished. On the Hibiya and Oedo lines.
F) Akihabara
Any introduction is probably unnecessary for anybody even mildly geeky; this is one of the two largest electronics areas in Japan (the other's in Osaka). In recent years, it's changed to cater to a broader variety of people, including people over-interested in anime (Japanese animation - that photo is from inside the station, by the way), eroge (erotic computer games), young girls dressed in maid costumes, and with the recent opening of the huge Yodobashi Camera electronics store, possibly more families (rather than the more traditional single male).
Obviously there's a lot more that could be covered in an article like this, but I hope I've given you an idea of what there is to see in Tokyo and how to get there.
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