Is there a MySQL message?

Nevermind. I found the setting: http://dev.mysql.com/doc/refman/5.0/en/server-options.html#option_mysqld_log-queries-not-using-indexes

matt: add an index for autoload, option name, or both?

Well in this specific case i just checked with this one parameter autoload for selection and setting an additional indey for this column.
Maybe its worth a check to do an explain select on this query with both types of indexes and an in case the index of both fields does fine, too just measure the qeuery speed.

the primary key is option name already. I think it makes sense to add an index on autoload, to help the query autoloading the core _option values.

Given how _option is used in product, storing settings for websites and users, this suggestion makes sense.

(In [3696]) Page titles report improvements fixes #1898

• new fields in 2 log tables (major schema upgrade in next release!)
• code refactored and optimized,
  (only the UI to display top entry/exit page titles is missing)

Performance improvements

• Actions Archiving is much more efficient, removed many JOINs and updating algorithm so that we select and parse action names only once per action.
• Fixes Action datatables should use integer indexes rather than string indexes (smaller size and faster access) #1600: datatables now indexed by int, no data migration but code works with both old and new data structure
• Fixes Missing index in mysql table piwik_options #1780: new index

Improvements to integration tests

• never loads the Provider plugin in proxy-piwik.php since reverse ip lookup slows up tests a lot
• fixing a test result that were previously incorrect (_withCookieSupport) because a static cache wasn't cleaned after each test