[I'm only familiar with these projects after they existed, happy to be corrected if my reconstruction is wrong]
I _suspect_ MultiMarkdown was the first. It started out as a fork of Gruber's Markdown.pl, and IIRC the whole point of "multi" in the name was the novelty (at least in context of markdown) of having multiple output formats, including LaTeX.
Surprisingly however, early versions until 3.0 emitted LaTeX (including math!), by XSLT conversion from HTML including MathML!
From there, math support spread to many other implementations, with experimentation both in source syntax and output techniques...
(MultiMarkdown itself switched formula input syntax from AsciiMath to TeX, and changed delimiters.)
Early
markdown extensions were pretty much free-for-all. Projects emulated
other projects but there was no formal standard (othen than Gruber's
original doc, which was effectively frozen), and no central place to
coordinate.
FWIW
https://github.com/cben/mathdown/wiki/Math-in-MarkDown has no timeline but lists _a lot_ of implementations with _some_ math support. Incomplete, by this point I would not be surprised if it has less than half of implementations out there. (It's a wiki, additions welcome!)
As any github wiki, it has git history which (very roughly) correlates with order of appearance — but mostly the order in which I found time to investigate them... Bias: tools I had no access to, such as Mac-only ones, are less present and more lagging.
I don't know if Pandoc was 2nd or later with math support, but it
was certainly widely influential — it set a high bar both in breadth and
qualify of markdown extensions 👏, so I expect most people extending markdown later, in any direction, were at least aware of it.
Some sites within Stack Exchange also adopted $math$ support (I guess
mathoverflow was the first?) which also must have been influential in
the communities using formulas.
* See my wiki, there is curious inconsistency with
electronics.stackexchange.com, they alone chose \$...\$ for inline. Not sure what to learn from that case, perhaps that inter-operability was valued less than suiting particular community's situation.
Then CommonMark appeared (jgm, thank you again ;-). While the spec itself is focused on nailing down original syntax + few very central additions (e.g. fenced blocks), it did provide a shared forum where people interested in markdown can collaborate on harmonizing syntax extensions.
Math has been discussed a lot:
As for GitHub's announcement, I'm happy they're recently adopting popular extensions (such as Mermaid), though I wish they sent some kind of "intent to implement" on commonmark forum ahead of shipping.
Due to their weight in markdown space, any syntax they adopt is likely to become The definite syntax...