Take a look at the Presence Web Service APIs, i.e. getPolledPresence. This interface is designed for server-to-server type integrations like what you are describing.
You could also use XMPP, e.g. by connecting your sever as a presence user and using ad-hoc presence subscriptions to check the status of other users.
- login - login as application user and get a session key
- login - login end user using the session key and get another key for end user
- getPolledPresence - get status of other users using the end user's key