Well, this depends on which version of Lotus Sametime you are using. Before version 3, this was not possible at all, other than build a new API yourself. However, since version 3.x of Lotus Sametime, IBM/Lotus has, on the request of many developers, extended their development toolkit(s) to provide means to change the buddy list. A new Redbook has been published, which discusses this feature as well.
Related Q&A from Hans Van Der Burg
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