ergophobe - 7:12 pm on Mar 6, 2013 (gmt 0)
I haven't looked at Wordpress internals for a while. Are you using MyISAM or InnoDB tables?
If you install this on another machine, say your local workstation or some cheap shared hosting, do you have the same problems? By default, mysql ships with completely unacceptable options for InnoDB tables. If you are setting up the server yourself, you MUST tune your InnoDB settings, otherwise MySQL will do a huge amount of I/O and slow to a crawl.
- plugins - might help, but I gather not. Still, if you have adequate server permissions, you could enable the slow query log. Sometimes a plugin can add a complicated JOIN that will slow things down a lot.
- memory - this should be more of a crash when out of memory thing assuming that it's actually just a wrapper for the PHP memory limit setting.
- unused rows in wp_options - 1MB still sounds excessive for the wp_options table (or is that your whole DB?)