Sandra raises some of the issues with presence aware applications like IM, but does not seem to provide solutions. This might be because solutions involve you naming vendors. She provides a summary of most of the issues:-
What are the ramifications for bandwidth, especially when you tie in instant Web videoconferencing and IP telephony calls? Do you have the budget for software licenses and gear to outfit the whole company? How will all this communication be monitored for compliance and auditing purposes? Do you have adequate enterprise storage silos and filtering tools to handle real-time transcripts? If they are to be used for business, then they are held to the same standards of record-keeping as e-mail and other types of business communications.
These can be broken into four areas, bandwidth, budget, security, and auditability. The first two are related in that you will need budget for bandwidth and software. As long as you control they types of collaboration, ie limit video or VOIP then bandwidth should not be an issue for most organisation. As soon as you move towards video or VOIP then bandwidth is an issue and needs to be professionally reviewed, ie by the IT department.
Security and Auditability are two massive issues that should not be under estimated. However there are products in the marketplace that can help provide “proxy” like servers that sit on your network to ensure security and keep track of all IM messages. I have a couple of posts that cover some of these issues and links to vendors who provide some third party solutions (ie non-Microsoft).