iCloud Notes not syncing
Updating OSX to El Capitan resolved the issue.

Update:

Just to clarify. The issue started when I updated my iPhone to the latest version (ie IOS9). A notification popped up saying my iMac's would also need to be updated to IOS9 to remain compatible which is likely a bug as my iMac doesn't run IOS (Ie should have said OSX 10.11 El Capitan).

At the time I wrote this question I wasn't aware that OSX had just released a new version.

From what I can tell, Notes.app has received a big overhaul in the latest IOS/OSX. Looks like they're on the warpath to kill and replace Evernote. Either way, the new features aren't available in older versions.

Looks like their syncing strategy is to continue syncing the old version of notes between devices but (eventually) cut iCloud.com support.