Don't worry about that. I have no intention of overstaying or running afoul of anyone!

Tokyorich..

Not a bit of it. I don't think badly of folks who push their luck. Quite a lot of the discussion on Flyertalk is dedicated to "tricking the system" - and jolly good fun it is, too. But the consequences of screwing up while attempting to exploit a mistake fare or maximize your rewards in the Intercontinental Hotels Priority Points program are rather less severe than the consequences of miscalculating your business with the immigration folks at NRT.
You seem to want to find a way to spend an extended time in Japan. Truly the best advice that you can get (and you did get) is that you should get a visa that permits you to spend an extended time in Japan. There are several approaches that might work - One would be to visit an English school, take a job as a "foreign language conversation teacher", get them to sponsor your visa - and then quit (unless you want to keep the job).
Here are a couple of Baldrick's cunning plans to help you out:
http://youtube.com/watch?v=mpyEnN9Ct2Q (about 40 secs into the clip)
http://youtube.com/watch?v=mpyEnN9Ct2Q (about 6 minutes into the clip)

BTW - If you're looking for front line stories of successful visa runs, I can't help you. But I can tell you that I had the experience of being called for "secondary interview" by immigration officials in two countries.
In both cases, I was doing nothing illegal, my story was convincing and the immigration people allowed me into the country. But in one of those cases, they put a flag next to my name in their system and every time I enter that country, I get called for a secondary interview (nine years later). Basically, the lesson I learnt was that you don't have to be doing anything illegal to fall foul of the immigration authorities. Immigration officers can deny you entry just if they think that you're intending to do something that doesn't match your visa status.

My partner's company is in the process of getting me a visa. Meanwhile, what I am trying to do here is nothing more than trying to proactively get some opinions and anecdotes about what may be considered OK or not OK by the authorities. As mentioned, I'll be traveling often, and my stays in Japan won't be anywhere near 90 days at a time, mostly just a few days or a few weeks. That's why I had asked about visa runs, as I got the impression from earlier discussions here that that is a definite no-no, and I wanted to get an idea if shorter stays would also be considered visa runs and frowned upon.

I had no idea that my simple questions would cause some of you to miscontrue that I am trying to beat the system or do anything illegal. I am merely trying to get an idea as to what may raise scrutiny to make sure that, until my visa has been obtained, I don't have to worry about frequent trips in & out of Japan.

Thanks for the suggestion - I'll look into it. Hopefully the company will get me something soon; they've been taking their sweet time in deciding what type of visa to get me.

I can't imagine what decision there is to make. Assuming your husband will be on some type of working visa you would then be on a dependent visa. Tell them to extract the digit.

If only life were so easy! We're (same-gender) domestic partners, a status not recognized in Japan. The HR dept has been procrastinating, thinking there's plenty of time till my 90-day runs out. They're now talking about getting me a business visa, in conjunction of consulting work they want to hire me for.

Righto then, my apologies if I made you reveal more about your domestic arrangements than you might have wanted too.
In your case you'd probably be better off organising your visa for yourself. Jib71 above made some good suggestions. If you have a university degree you'll have no problems. In the short term, enrolling in a Japanese language school will give you a visa and you can work up to 20 hours a week, which is plenty assuming your hubsand is on a decent ex-pat package.
Just something about visas too- there are often no real rules it seems, just guidelines. Might be worth going down to your local immigration office, lay all your cards on the table. You never know what kind of creative visa arrangements they might be able to come up with. Of course this could back-fire, though I think it is unlikely too.

Not a problem, and thanks for your suggestions. Luckily my partner's firm has full recognition and spousal benefits for domestic partners. After a slow start and a long delay, attributable mainly to the HR staff vacations and other more urgent matters, they are now paying full attention to my visa issue. Hopefully they'll come through. If not, I'll explore some of the ideas on here.

My impression is that Japan is pretty repressive on GLBT issues so I don't think I'd recommend what valve bouncer suggests: going to immigration and "laying all your cards on the table" without some prior indication that it was going to work. The ideal way for your company to handle this problem might be to hire a Japanese immigration specialist who previously worked for the immigration department (this is sometimes called "amakudari" or "descent from heaven" in Japan).

If your company's HR department does NOT have local expertise in this issue there is a possibility that they could screw it up for you, so warn them in that case to proceed carefully.

FYI in my experience...

I usually "enter" Japan 6-8 times a year.
I make 4 quarterly trips and usually enter once and again if I left baggage in storage at NRT while in BKK.
So technically I have essentially full yearly coverage with my visitor's visas.
But I'm there in country only about 30 days a year.

It really must have something to do with the time in country. THey can see your ins and outs.

I've never been hassled although my passport looks like a stamp collector's book filled with Japanese visas.

Scho

I believe they're working with an immigration specialist, but I'll warn them anyway. Thanks for the heads up.

Thanks, Scho, for this input - exactly what I was hoping to hear about. This makes sense, i.e. they track the amount of time you spend in the country and are not as concerned about how many times you come in & out.

On the other hand, if schoflyer were to be ever stopped and questioned, he could explain himself without any trouble, so he can take all the risks he likes, he's clean.