Sure they are. They're a CA, the clients are just for users' convenience. Anyone who wants to can write their own client against the LE rest API.
Possible there is support for Windows and IIS, but their own website strongly suggests otherwise.
EDIT: if they consider their client and their CA as two different products, well, right now the website conflates the two badly. And there's absolutely nothing there to suggest it supports Windows/IIS.
> And there's absolutely nothing there to suggest it supports Windows/IIS.
Their "system" is an API for issuing certificates. There's nothing platform specific about that.
> right now the website conflates the two badly.
From https://letsencrypt.org/getting-started/: You’re welcome to use any compatible client, but we only provide instructions for using the client that we provide.
Edit: This is the protocol they use: https://github.com/letsencrypt/acme-spec
I found the link here: https://letsencrypt.org/how-it-works/
Now I'm just confused.
But I still say: if their mission is to make it as easy as possible to install a SSL cert on any website, as long as they don't have any (apparent) support for Windows/IIS, they're a long, long, long way away from fulfilling that mission and probably shouldn't be leaving beta.