1. Tell me a bit more about your environment. How many users? How many servers? When are your replication events occurring. Excessive replication may be occurring during this time span. Set most jobs to LOW PRIORITY.
2. How many full-text indexes are there on the server. The indexing process is very memory intensive and could be bogging your server down.
3. When did the problem start? Has the environment ever properly worked? What has changed from then?
4. Why not go to Version 7? The Notes kernel in our small environment has been much more responsive, and we only have transitory (1 minute) drops in our server availability index.
5. In Domino Administrator under the server tab, under the monitoring tab, What processes stop during this crucial time period?
6. What does the server log tell you about what is happening during this time period?