The fix for Domino running on Windows server is to install the IBM HTTP Server (IHS), which is now included with the Domino 9+ install (but is not installed by default). It is a special version of IHS intended to sit as a proxy in front of the Domino HTTP server and handle SSL/TLS.
I installed it over the weekend on a 9.0.1 IF1 server. It is a lengthy and tedious process, but it is working great now and my site tests secure using the neat Qualys SSL test: https://www.ssllabs.com/ssltest/index.html
I used these various resources:
Three step process from Darren Duke that uniquely shows a way to convert your existing Domino keyring (*.kyr) certificates to the format needed for IHS. It requires the ability to run one of the key generation programs under Win XP or XP mode on Win 7. This is what I used:
http://blog.darrenduke.net/darren/ddbz.nsf/dx/ibm-domino-now-includes-ibm-http-server-but-how-do-you-find-it.htm
http://blog.darrenduke.net/darren/ddbz.nsf/dx/exporting-domino-ssl-keyfiles-to-another-format-for-use-with-ihs-.htm
http://blog.darrenduke.net/Darren/DDBZ.nsf/dx/setting-up-ibm-http-server-to-redirect-all-traffic-to-https-when-fronting-domino-i-guess-this-is-part-3.htm
Three step process from Russell Maher that shows the default IBM method of requesting and installing an SSL key in the correct format. I referenced this a lot, but used the key generation process from Darren Duke above:
http://xpagetips.blogspot.com/2013/05/setting-up-ibm-http-server-with-domino-9.html
http://xpagetips.blogspot.com/2013/05/setting-up-tls-ssl-for-ibm-http-server.html
http://xpagetips.blogspot.com/2013/05/setting-up-tls-ssl-for-ibm-http-server_30.html
Various IBM instructions and sites about setting up IHS, from which the two gentlemen above used as a starting point to customize and give helpful screenshots. I read all these and compared them to the procedures from the blogs. More technical and and detailed, but less friendly for actually getting the job done (especially if you want to convert your Domino kyr SSL cert):
http://www-01.ibm.com/support/docview.wss?uid=swg27039743 (read the PDF)
http://www-12.lotus.com/ldd/doc/domino_notes/9.0/help9_admin.nsf/855dc7fcfd5fec9a85256b870069c0ab/caa25dc9fd95076b85257b19005b3894?OpenDocument&Highlight=0,Installing,the,IBM,HTTP,server,module,to,support,TLS
http://www-01.ibm.com/support/docview.wss?uid=swg21612316
http://www-12.lotus.com/ldd/doc/domino_notes/9.0/help9_admin.nsf/b3266a3c17f9bb7085256b870069c0a9/3703294d1a3a2bc785257b19005b3896?OpenDocument
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The "official" IBM response should be to either a) update the Domino SSL stack to the latest and greatest. Don't hold your breath, but it is loooong overdue, or b) make the IHS install seamless, transparent, and the default. It should appear to be a monolithic part of Domino and take over the HTTP functionality fully from here forward. We should not even know it is actually IHS, and be controllable fully from inside Domino.
While IHS works and I appreciate that we Windows Server customers have a decent fix , it feels like a kludge and takes way too much admin attention and detail to set up, especially if you have multiple site docs.