MediaWiki slow save of edited pages
Are you logging slow queries in mysql? Does the mysql error log show anything?
In circumstances like this I would start looking at Cacti. The mysql-cacti-templates from Percona are invaluable for this. You will be able to see if you're experiencing an IO issue or a table locking issue. There could be quite a few causes.
Refs:
http://code.google.com/p/mysql-cacti-templates/