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Most often referred to in Japan as an MVNO, which stands for "mobile virtual network operator," the following is a potentially-growing list of SIM-only mobile providers that resell services on one of the major Japanese mobile networks: NTT Docomo, Au by KDDI, or Softbank.  While the big three Japanese providers will usually force you into an over-priced 2-year auto-renewing service contract inseparable from the bundled phone, MVNOs can and will sell you just the SIM card and service.  Most resell NTT Docomo, and I have yet to see one that resells Softbank; however anything is possible as Japan looks as if it is finally embracing SIM-only solutions.

* I focus solely on providers offering full phone service, as in a real phone number.  There are countless other Japanese providers offering data-only SIMs, and I don't bother researching these because I myself want and need a real phone number.  Yes, my research efforts wallow in self-interest.
* Price isn't everything.  Be wary of service term obligations and what other people are saying about their data speeds.  While one provider may be less expensive, another provider may have a shorter service term obligation.  I may be willing to pay a little more if I know I can ditch them sooner if their service is subpar.
* Pay attention to what phones and features (like tethering) they support--they almost always provide a list on their site (search for something like 動作確認端末一覧 or just 端末).  For example, at the time of writing, UQ Mobile states they do not support newer iPhones.  Bummer.

NTT Docomo Resellers
Asahi-Net - asahi-net.jp/en/service/mobile/sim/
Asahi-Net is currently my mobile provider of choice.  I previously sang Asahi-Net's praises as a solid English-speaking ISP (Life in Japan - English-Speaking Internet Service Provider Asahi Net), and now they offer mobile SIM cards as well.  As Asahi-Net caters to the foreign crowd, they have an English website.  However, they do mention that you will may need some Japanese skills to complete the sign-up process.  Asahi-Net offers discounts to referrals, so please provide my Asahi Net user ID if/when you sign-up --> sb8d-pvln

B-Mobile - www.bmobile.ne.jp
This the the one I have blogged fairly extensively about because it's the only one on this list that yours truly has actually used.  B-Mobile is one of the first and only providers to offer full phone service, and they have an assortment of SIM-only libations.  Their pricing is fairly competitive, their obligation term is on the short side, and their web interface is user-friendly--provided you (or a friend) have decent kanji skills.  They also have an English-speaking helpdesk, but I honestly don't know how good it is since I've never used it.  My primary complaint is echoed by numerous Japanese reviews and forum posts--their data speed sucks.  So far I've tolerated it because I have wifi at both my home and office, but now that other SIM-only providers have entered the market, it may be time to move on to more rapid rivers.
Amazon Japan - B-Mobile

DMM - mvno.dmm.com
DMM is another one of those companies involved in various business model strata, so they too have entered the MVNO game.  A good friend of mine signed up with them and reported that their data speed is "pretty good."
Amazon Japan - DMM Mobile

IIJ - www.iijmio.jp
IIJ has been in the data-only SIM game for a while and recently expanded their SIM portfolio to include full phone service.  I've never used them, but my friend has.  He said their data speed is superior to B-Mobile's, which means they probably don't over-subscribe their bandwidth like B-Mobile tragically does.  Bic Camera also sells Bic/IIJ-branded SIMs in their stores (see this: http://www.biccamera.com/bc/c/service/bicsim/), which may smooth the application process for those that fear kanji.
Amazon Japan - IIJ

Rakuten Mobile - broadband.rakuten.co.jp/rmobile
Rakuten sells freakin' everything, and now they even sell SIM-only mobile service.  I've previously espoused Rakuten in my podcast, graphically expressing how I have a serious heroin-like drug addiction to Rakuten points.  As I seek ever-increasing ways to engorge my Rakuten account with even more points, I may indeed pull the trigger on them and sample their service quality.  Unfortunately, they enforce a 1-year service obligation.

I have zero experience with the following providers.  I include them merely to be comprehensive because I'm OCD that way.  Note how I even put them in alphabetical order.

Biglobe - join.biglobe.ne.jp/mobile/lte
Biglobe is owned by NEC, a big Japanese tech company--the guys that made the TurboGrafx-16 game system.  Anyone up for a quick game of "Bonk's Revenge?"
Amazon Japan - Biglobe

Freetel - www.freetel.jp
For a company with "free" in the name, their prices sure are high!  Bad jokes aside, I don't know much about them other than the fact they seem to be a phone manufacturer as well.
Amazon Japan - Freetel

Hi-Ho - home.hi-ho.ne.jp/hihomobile/lte/d
I find Hi-Ho attractive because of their name.  I could then tell everyone that my mobile provider is Hi-Ho.  It's the provider of choice for hip-hop-styling dwarf pirates.

Nifmo - nifmo.nifty.com
Nifmo is run by Nifty, which is owned by Fujitsu, makers of laptop computers and other stuff.  Did you get all that?
Amazon Japan - Nifmo

OCN - service.ocn.ne.jp/mobile/one
OCN is run by NTT Communications, which is owned by NTT.  Yep, the big guy himself.
Amazon Japan - OCN

So-net - www.so-net.ne.jp/access/mobile
This one is owned by Sony--the guys that made those portable tape players we all knew and loved.  I for one listened to my "Fat Boys" tape non-stop on mine.  Good times, dude!
Amazon Japan - So-net

U-Mobile - umobile.jp
U-Mobile's website has a very cute girl on it.  I'm (just a little) ashamed to admit that this is a huge selling point in my book, and that I spent much longer perusing their website than the others.  I did happen to notice that their service obligation is 6 months, while most seem to go with 1 year.
Amazon Japan - U-Mobile

Au by KDDI Resellers
Mineo - mineo.jp
Mineo is one of few that resells KDDI's service, making them unique in that sense.  My friend uses them with his Android phone and has been thoroughly satisfied with their data speeds.  Pay attention to their phone support, as they only recently started supporting newer iPhones: http://mineo.jp/device/devicelist/au/  Depending on the phone, things like tethering may not work.
Amazon Japan - Mineo

UQ Mobile - uqmobile.jp
Not to be confused with U-Mobile, UQ Mobile resells Au's service, which makes sense since KDDI is a key shareholder.  I was pleasantly surprised that they even have an English version of their website.  Unfortunately, they don't (yet) support newer iPhones (see this: http://www.uqmobile.jp/product/sim/devices/).  What's up with that?
Amazon Japan - UQ Mobile

Further Reading
My warm regards go to this Japanese site that provides loads of SIM-only related info: www.mvno-navi.com.  Specifically, this page lists MVNOs sorted into various useful categories: http://www.mvno-navi.com/mvno-list.

Final Note
It's not common to find these SIM cards for sale in brick-and-mortar shops, so you'll likely have to purchase and apply online.  However, if you're staunchly determined to purchase and apply in a real shop with real people (and/or your kanji reading skills suck like mine do), then I'd suggest visiting large stores like Bic Camera and Yodobashi Camera.  I'm quite sure they do carry them.

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