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Yes, we enable slow query logs from time to time, look at those and try to optimize for those. MyISAM tables.

We've been cycling frequently (and painfully) through (2) (and less frequently through (1)) for the best part of three years now, so please don't accuse us at least of looking for a quick fix :)

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With MyISAM tables you could have integrity problems. And if you are mixing innodb and myisam you are splitting buffers memory that well could go to just one kind (i.e. most memory for innodb) if you switch to that. If innodb is slow in insertions, you could try using TokuDB as storage engine, that is pretty fast in that and have a bunch of advantages. And if you are using MyISAM for some particular feature (i.e. full text indexing) MySQL 5.6 already have it in innodb, or you can separate that search to a sphyinx server.

Thanks. We'll check out TokuDB.

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