Tokyo is the capital of Japan.
It is almost impossible to hitch out of Tokyo or any large Japanese city by waving your thumb on the Ginza. Thus, to get out, you have to find the places where drivers going out congregate, which in practice means service areas (サービスエリア sābisu eria, SA) or parking areas (PA) on the large toll expressways (高速道路 kōsokudōro) connecting Japan's major cities. As you might guess, service areas are larger and better equipped than parking areas, but surprisingly few Japanese are familiar with the difference so it's easier to label them all service areas.
A useful rule of the thumb (pun intended) is that if you can get somewhere on a train for less than 2000 yen, hitchhiking the distance is unlikely to be worth the trouble. For destinations around Tokyo, such as for Mount Fuji, Hakone, Nikko, hitchhiking is unlikely to be worth the trouble... until you actually get there, that is. All three regions have expensive local transport but plenty of unhurried tourists driving about, always a good combination for the hitchhiker.
How to get out of Tokyo
Lots of expressways radiate off Tokyo's local highway system (首都 shuto). So what you want to do is pick a destination, match it to an expressway, and get to the closest PA/SA. Here's the list in clockwise order from west to east, you will probably find it useful to consult a 1:10000 Japanese map to get your bearings. Most English highway signs will not distinguish short and long vowels, but your driver will, so pronounce it right!
A preliminary notes about buses: in general, Tokyo's commuter bus system sucks. They run very infrequently (typically 1/hr in the boonies), have a lunch break of several hours, and stop running early. Try to get to the bus station before 11 in the morning, or you'll probably have to wait until 2 in the afternoon for the next one!
Tōmei Expressway (東名)
Directions: Go to Tōkaichiba (十日市場) station on the JR Yokohama line through any one of a number of connections (Shibuya to Nagatsuta via Tokyu Den-en-toshi, Shibuya to Shin-Yokohama via Tokyu Toyoko, Shinjuku to Machida via Odakyu, etc.) The train trip is only 30 minutes, but it's a couple hilly kilometers to the PA, so consult an area map before you set off. You must head EAST along the expressway, expect to take 30-40 minutes from the station. First you underpass the expressway, cross the river, and than follow back towards Tokyo until you find over-fly bridge over express way again which takes you to your PA South.
Chūō Expressway (中央)
For: Fujiyoshida, Lake Kawaguchi, Nagano, Gifu, Nagoya & western Japan (slow route)
Where: Ishikawa SA (石川)
Where not: Takaido IC (高井戸, near Keio Inokashira/Takaido stn.) or Eifuku IC (永福, near Keio/Meidaimae stn.), both way too busy
Cost from Yamanote line: ~800 yen
Last verified: August 2000
Directions: Get to Kichijoji (吉祥寺) via Keio Inokashira from Shibuya or JR Chuo from Shinjuku, switch to JR Chuo (preferably a kaisoku commuter express to Takao, otherwise you'll have to change trains a few times) and go to either Toyoda (豊田) or Hino (日野). From Toyoda station (north exit), take Keio bus 日04 from platform 2 to Ishikawacho-higashi (石川町東). They run from 7:35 to 18:15, usually at 35 past the hour, but there is no 12:35 bus. The same bus runs to Hino station so you can catch it from there too. The distance is about 3 km and the bus route is reasonably straightforward, so it is also walkable if you're in the mood.
Once at Ishikawachō-higashi, backtrack to the lights (I'm assuming you're coming from Toyoda), you'll see the highway on your left. Go to the highway, but not under it -- turn left, up the hill, then open the gate that you are not supposed to open, walk up to the SA fence and jump over the one-meter gate if it is locked. You're in!
Note: Chuo branches a few times, be sure you know what branch you want to go to and what branch your driver will go to. The first is Ootsuki Junction (大月), where the road splits between the Nagano and Fujiyoshida branches; the last SA before the junction is Dangōzaka (談合坂).
Kan'etsu Expressway (関越)
For: Niigata, Sado Island, Japan Sea coast
Where: Miyoshi PA (三芳)
Alternative: Nerima IC (練馬), approx 1 km from Seibu Ikebukuro line (西武池袋線) Shakujii-kouen (石神井公園) station
Cost from Yamanote line: ~500 yen
Last verified: April 1998
Directions: Take the Tōbu Tōjō (東武東上) line from Ikebukuro to Tsuruse station. From the station, take Raifu Basu #4 to the Sentoraru Byōin (センとラル病院) stop, as usual it runs once per hour except during lunchtime. The bus will deposit you on the wrong side of the parking area, cross the bridge to get to the side going away from Tokyo. Alternatively, you can walk the 3 km or so from Fujimino station; there should also be a bus from Fujimino, but it didn't seem to exist...
Tōhoku Expressway (東北)
Directions: Go to Hasuda station on the JR Utsunomiya (宇都宮) line, starting from Shinjuku or Tokyo. Take the east exit and locate platform #3, take Tōbu (東武) bus #4 to Shiyakusho-mae (市役所前). Right before the stop the bus actually goes under the expressway, return to the bridge (don't go under it!) and head a few hundred meters up the hill/to the north along the expressway until you reach the PA. The gate may be locked, but the fence is low and jumping over it is no problem.
Jōban Expressway (常磐)
For: Mito, Iwaki, Sendai (slow route)
Where maybe: Mukōjima IC (向島) up the riverside and across the bridge from Asakusa or Kahei PA (加平) from Kita-Ayase (北綾瀬) on Eidan Chiyoda subway, both on Shuto 6 connecting to Jōban
Where not: Moriya SA (守谷)
This highway is the bane of the hitchhiker, as there appears to be no decent way of getting onto it. The nearest real service area, Moriya SA (守谷), is way out of town, at least 3 transfers plus a bus ride from the Yamanote. The IC and PA listed above are unexplored possibilities. One sure way: take a ¥2000 train to Mito and start there...
Warning: If you get on at Mukōjima IC, the road soon joins Shuto C2, after which C2 branches off again towards the Tōhoku Expressway. Make sure you know where your driver is going!
Higashi-Kantō Expressway (東関東)
What, you're going to hitchhike to catch your flight!? Do yourself a favor and take the train, Keisei'll get you there for 1000 yen. If you insist, you could try to catch the Expressway Bayshore Line (高速湾岸線) from Odaiba or Shin-Kiba, which transforms into the Higashi-Kantō.
Getting off in Tokyo
95% of the time, once on the expressway, getting back to Tokyo is a piece of cake: your driver is also going to Tokyo, so he'll drop you off at the nearest train or subway station, and you can find your way home. Problems arise the other 5% of the time, when your driver is going either through Tokyo or to a part of Tokyo extremely far from your part of Tokyo. What to do?
Your driver may exit the expressway just so you can get off, but this is a waste of time and money for him, as he has to fight his way back and pay an extra toll, so don't count on it. The driver may also try to drop you off at a toll booth or at an interchange, which will either get you in hot water from the authorities or dead from being hit by a car. The least of three evils is thus getting dropped off at a service area.
Moral of the story: when near a big city, feel free to reject rides that aren't going close enough. There will be more.
Shuto Service Areas
If the service area is one of those listed above, you know how to get back. If not, you have been left at a service area not listed for a good reason. Almost all the 15+ parking areas on the Shuto are tiny (space for around 20 cars max), suspended multiple stories above the earth with entrance/exit possible only through staff quarters, and inconviniently located to boot. However, as getting out is a lesser crime, you may be able to sweet-talk somebody into unlocking those staff-only doors and letting you out, as long as you promise not to come back in.
The Shuto network is an indecipherable tangle that looks vaguely similar to the Tokyo subway system, except that most stations are accessible only when going in one direction and you have 5 seconds to decide whether to exit. The parking areas are omitted from most maps, only specialty maps will usually show them. One convention worth learning quickly: all routes and lanes going towards the center are nobori (上り, going up), whereas routes and lanes exiting Tokyo are kudari (下り, going down). The majority of Shuto parking areas are nobori-only, a small saving grace for the hitchhiker coming in, but yet another reason why they're useless for exiting Tokyo.
At any rate, I've only ended up in this situation once so far, so here's the beginning of a new list, sorted by route number.
Shuto 3 (高速3号)
Connecting to: Tōmei
Shuto 4 (高速4号)
Connecting to: Chūō
Eifuku PA (永福)
Access: Nobori only
Last verified: Never
Small. Somewhat oddly located right next to a row of tollbooths and an exit (which thus cannot be used even illegally, since they'll spot you if you try to walk it!). If you do find your way out, Meidaimae station at the crossing of both Keio lines is nearby (ask for directions).
Yoyogi PA (代々木)
Access: Nobori only
Last verified: August 2000
A pathetic one-lane excuse for a parking area quite literally suspended three stories above the earth. Climbing over the fence would be easy if the drop weren't likely to kill you; there's also an expressway entrance nearby, but as noted earlier, walking on it is highly illegal and dangerous to boot. The third option was shown to me by a janitor to whom I pleaded my distress: at the furthestmost tip (from your arrival point) of the building is a door, which leads to a staircase, which leads outside. The doors along the route may, or may not, be locked. Once you do get out, one block straight and a few to the right will get you to Yoyogi station on the Yamanote/O-Edo lines. (Odakyu line Minami-Shinjuku station is also nearby.)
Note that it might theoretically even be possible to get into the PA this way, literally through the back door, but I wouldn't recommend it -- if the doors are locked you're out of luck, westbound is towards Tokyo, not out of it, the Shuto splits into about 17 different directions soon after the PA, and the PA deservedly gets little enough traffic as it is. And you'll annoy the friendly janitor.
Shuto 6 (高速6号)
Connecting to: Jōban
Kahei PA (加平）
Access: Kudari only
Last verified: Never
Located inside a highway entrance spiral, this one may actually be accessible from the ground. Kita-Ayase (北綾瀬) station on the Eidan Chiyoda subway line is about half a kilometer to the east along the large road that crosses under the highway between the entrances.
Connecting to: Tōhoku, Jōban
Shuto S1 becomes C2 and merges briefly with 6 before splitting off again and heading off to Tokyo Bay. Confused? You will be.
Kawaguchi PA (川口）
Last verified: July 2012
The PA is only on the side that goes back to Tokyo. If you're trying to go to Tōhoku, you need to get on the Tōhoku-dō.
Tokyo Gaikan Expressway (東京外環自動車道)
Connecting to: Kan'etsu, Tōhoku, Jōban
Niikura PA (新倉）
Access: Both directions
Last verified: Never
Small. Close to Wakō-shi. Often omitted even from highway maps since it doesn't belong to either the kousokudouro or the shuto systems!