I don't see what the formerly "Standard Markdown" project has done to accomodate Gruber as something done because they accepted that he had a legal claim that they were required to comply with, I see it as something that they did because they thought he made a demand that, whether or not it was mandatory, they felt it was reasonable and appropriate to comply with to the extent reasonably practical without tying things up for the project in an open-ended way.
Its not clear to me that Gruber has any basis for a claim in court here:
1) Its not clear to me that the license applies at all, in that its not clear that writing an spec that abstracts and regularizes the common behavior of several programs (which may or may not be all legally derivative of the one at issue) is a non-fair-use derivative work of the program at issue under copyright law, such that a license for that program would be required,
2) Further, its not clear to me that, aside from the copyright license on markdown.pl, that markdown was ever a trademark and, if it was, that it hasn't been either abandoned or genericized.
Of course, Gruber can sue and try to establish any basis for preventing the use of the name that he'd like.
Trademarks depend, I dunno the details. Knowing that would help.
The actual question is whether Markdown has indeed become so generic in programming that it no longer holds a copyright.
I think, yeah, maybe, since there is a standards movement going on.
The process expressed in the code could conceivably be patented, but he's taken no steps to do so to my knowledge. He freely and openly admits that the formatting syntax of Markdown is derived from existing de facto conventions, so good luck to anybody who tries to patent that.
The name "Markdown" could be trademarked, but he never did. Even if he had, his trademark would likely be invalid (genericized) since he has never enforced it.
The former is a standard spec and test suite about derivatives of Markdown, some of which have basis in implicit and explicit blessing to use the name "Markdown." I'm not sure claim to the name makes sense in the spec definition is a valid claim, though.
It would be like requiring every author to specifically request official blessings to write about trademarked (registered or not) subjects. That'd be silly as it falls well within fair use of the name. The name "Standard" or to a lesser degree "Common" complicate ownership, certainly. I think I would have preferred the verb instead: "Standardized." Regardless, "Markdown" is the subject of the spec, not necessarily the product.
The latter implementations, however, probably shouldn't use the name Markdown in them at all if Gruber doesn't want them to use it. They really don't need to exist in the spec. They're just examples of valid interpreters. Spin them off and rename them, leaving the spec and tests.
What's clear to me in all of this is there is value in portable markdown that will parse the same across applications and services, whether we call it markdown or not.
The drama of it all is amusing, in any case.
I don't think many people actually use Gruber's perl code.
If he wants to protect the format, I suspect he'd need a patent.