I would say that in my opinion things like the McCoy Great Northern freight set (25 or so sets made); McCoy Canadian TTOS freight sets (100-130 made); or the Williams 1979 TCA Silver Anniversary set (+- 200 sets made); some of the Richart sets of under 200 made: these kind of numbers sound to me like "low production". Especially since these date to about 30-40 years ago, and numbers extant have probably dwindled some.
Once you get up to 1000, given how relatively small the hobby as a whole is, I think you have to find another name for them; they don't flood the market surely, but there are enough out there that they are hardly scarce.
I would tend to equate the word "scarce" with the "low production" numbers. I like to reserve "rare" for steaks, or things that you have enough fingers to count. More "rare" than that are the one-offs or something that maybe two or three were made of; these I would feel comfortable calling "unique" or nearly so.
But I realize this is very arbitrary, and I'd respect any one else's approximation as well... as long as we don't descend to the eBay level of calling everything that isn't Lionel "rare".
Ives O Gauge Herald Boxcars are a case in point. It's quite hard to find them all, and may take years of searching. The temptation is to call the one you can't find rare or scarce, but the fact is they were made by the thousands, even tens of thousands. There has surely been some attrition over the years, but one has to presume they are out there. One seller has taken to calling these "tough" cars, as in "tough to find", to avoid the "S" or "R" words.
Arno, on your web site you make a distinction between "manufacturers" and "craftsmen". Seems to me that by definition, anything that can be called "low production" is still a production run, and is the province of manufacturers - McCoy, CMT, Forney, Williams... The "craftsmen" are basically handmaking things, like Jim Cohen or Joe Mania, and their output IMO isn't going to reach "low production" levels.