This exception was being thrown by Doctrine during a long-running process:

exception 'Doctrine_Connection_Mysql_Exception' with message 'SQLSTATE[HY000]: General error: 1205 Lock wait timeout exceeded; try restarting transaction'<br />

The code in question was performing a lot of queries within a transaction – it seems that innodb will only hold a lock for so long, and this limit was being reached before the transaction could commit and release the lock. The solution (other than refactoring the code to be a little quicker!) was to increase innodb’s innodb_lock_wait_timeout setting in my.cnf to accommodate the transaction.