We've just deployed Outlook Web Access (OWA) to authenticate with Yubikeys as a OTP.
Our solution integrates FreeRADIUS, ISA Server 2006 and Exchange 2007 with the Yubikey tokens. Uniquely, we have written custom RADIUS code to authenticate using LDAP against the AD and then the Yubikey Validation Server, meaning that we can store the user's Yubikey ID in the AD, and not in a local mapping file.
I have published a full overview of the solution here:
http://www.curiousmentality.co.uk/2009/09/yubikey-authentication-outlook-web-access/My company will be providing this as a full solution to future clients, as well as offering consultancy on the integration.
Regards,
Tim Creswick
Thoughtspace Ltd (UK)