The JR Group Companies
The heavily-subsidised Japanese National Railway (or Railways) was broken up in 1987 into the six regional companies plus JR Freight and two non-operating support groups (the Railway Technical Research Institute, RTRI, and an information systems group). After this, the seven operating companies individually made their way towards profitability by downsizing workforces and to a limited extent their routes. The Central Japan Railway Company (JR Central, also known as JR Tōkai for the largest portion of the region it serves) had a substantial revenue source in the original Tōkaidō Shinkansen route, while the East Japan Railway Company (JR East) had the densely-populated Kantō plain around Tōkyō. The other companies had a harder time of it.
As part of the transition the companies were first subsidiaries of government-owned holding companies, and eventually mad public with decreasing government ownership.
Of these companies, three are of interest for Tōkyō-area railways.
The East Japan Railway Company (東日本旅客鉄道株式会社)
The East Japan Railway Company, more commonly known as “JR East”, operates approximately 7,526 km of track, including 2,680 km of electrified narrow-gauge track, as of 2010, with over 52,000 employees, serving the Kantō region around Tōkyō and the northern (Tōhoku, meaning “northeast”) part of Japan’s main island, Honshū. This includes the commuter-heavy narrow-gauge lines around Tokyo.
JR East continued the work begun by JNR for a cost-reduced train design. This ultimately produced the 209 Series with maintenance costs 50% of those of the original 103 Series that had been the dominant vehicle in 1987. Later they produced the widely-used E231 series, with additional savings in operating costs. JR East has also continued investment in its infrastructure, with expansions to its Shinkansen lines in particular.
As of the company's 24th year (ending 31 March 2011), JR East had income of 254.5 billion yen (about US$3.4B) on revenue of 2,547.3 billion yen (US$34B), which is down nearly 6% over three years previously due to a long recession. The company remains profitable (net income 76.224 Billon yen, or about US$1B, and operates 6,377.9 km (3,963 mi) of narrow-gauge track and 1,134.7 km (705 mi) of Shinkansen lines (cf. English-language business report, PDF).
Although JR Central (a.k.a., JR Tōkai) doesn't operate conventional trains into Tōkyō (as far as I can tell) its Tōkaidō Shinkansen line terminates at the main Tōkyō station, and operation of these trains is shared with JR East in some fashion. As of its 2010 annual report (English-language) it had revenue of 1,486 billion yen (US$15.985B) and net income of 91.764 billion yen (US$986M), a revenue reduction of 4.7% from two years ago.
JR Freight has a few lines of its own, but mostly uses operating rights over JR East lines in the region around Tōkyō. It also remains privately-held by the government (via the Japan Railway Construction, Transport and Technology Agency, an "independent" but government-funded entity). It does, however, publish annual financials (English-language) and for the year ending 31 March 2010 reported "railroading" revenues of 137 billion yen (US$1.8B) with a net operating loss of 2.759 billion yen (US$37M). Compare this with a U.S. Class I freight railroad such as CSX (2010 revenue of US$11.255B with net income of US$1.355B).
Despite this smaller scale JRF continues to operate a fleet of hundreds of mainline diesel and electric locomotives, and has developed new models since it was split off from JNR, with at least 239 new locomotives constructed in that period.
In 1984, JNR ceased operating general freight, closing most of its general-freight yards (some appear to remain, particularly near ports). Since the split, JR Freight has continued the trend begun under JNR, focusing its efforts on unit trains operating between container terminals, both inland and at port facilities, with a few that operate between privately-owned endpoints. These are mostly domestic containers on special flat cars, but unit tank, gravel and other types also exist.