We were working with a customer the other day who had intermittent performance every day when people showed up to work (50k users). We erroneously made the assumption it was valid traffic and started looking at farm topology, using SSL accelerator cards, etc. Looking at the logs, I noticed indexing was occurring during this same time. Since the Index server had a 100MB link and most users were WAN users the index server was taking precedence.
This was easily resolved by changing Site Hit Frequency Rule in Search Settings. We set it to 1 simultaneous document with no delay. The default setting is 5 simultaneous documents with no delay in between.
-ben