I've noticed that the web server has been running slowly today.
Anyway I think I've found the problem. One of my old blogs sites is currently being spammed. Currently there are 3.3 million comments in the database!
EDIT: Problem fixed:
mysql> delete from comments WHERE id > 556;
Query OK, 3305122 rows affected (2 min 21.45 sec)
EDIT2: The spam has been coming from caravan.ru a Russian ISP (who's logo is very similar to optus' old one...).